rs119486097

Positions:

chr17-74763436-G-A

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_004252.5(NHERF1):c.673G>A(p.Glu225Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00308 in 1,614,038 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0033 ( 3 hom., cov: 33)

Exomes 𝑓: 0.0030 ( 22 hom. )

Consequence

NHERF1
NM_004252.5 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts P:2B:4

Conservation

PhyloP100: 4.63

Variant links:

Genes affected

NHERF1 (HGNC:11075): (NHERF family PDZ scaffold protein 1) This gene encodes a sodium/hydrogen exchanger regulatory cofactor. The protein interacts with and regulates various proteins including the cystic fibrosis transmembrane conductance regulator and G-protein coupled receptors such as the beta2-adrenergic receptor and the parathyroid hormone 1 receptor. The protein also interacts with proteins that function as linkers between integral membrane and cytoskeletal proteins. The protein localizes to actin-rich structures including membrane ruffles, microvilli, and filopodia. Mutations in this gene result in hypophosphatemic nephrolithiasis/osteoporosis type 2, and loss of heterozygosity of this gene is implicated in breast cancer.[provided by RefSeq, Sep 2009]

NHERF1 links:

NHERF1 (HGNC:):

NHERF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007968813).

BP6

Variant 17-74763436-G-A is Benign according to our data. Variant chr17-74763436-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 5272.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High AC in GnomAd4 at 510 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NHERF1	NM_004252.5 linkuse as main transcript	c.673G>A	p.Glu225Lys	missense_variant	3/6	ENST00000262613.10	NP_004243.1	O14745-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NHERF1	ENST00000262613.10 linkuse as main transcript	c.673G>A	p.Glu225Lys	missense_variant	3/6	1	NM_004252.5	ENSP00000262613.5		O14745-1

Frequencies

GnomAD3 genomes

AF:

0.00335

AC:

510

AN:

152268

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.000523

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.0205

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00378

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00344

AC:

859

AN:

249956

Hom.:

AF XY:

0.00319

AC XY:

432

AN XY:

135350

show subpopulations

Gnomad AFR exome

AF:

0.000559

Gnomad AMR exome

AF:

0.000377

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.0203

Gnomad NFE exome

AF:

0.00328

Gnomad OTH exome

AF:

0.00476

GnomAD4 exome

AF:

0.00305

AC:

4455

AN:

1461652

Hom.:

Cov.:

AF XY:

0.00303

AC XY:

2206

AN XY:

727114

show subpopulations

Gnomad4 AFR exome

AF:

0.000418

Gnomad4 AMR exome

AF:

0.000448

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0000464

Gnomad4 FIN exome

AF:

0.0199

Gnomad4 NFE exome

AF:

0.00287

Gnomad4 OTH exome

AF:

0.00270

GnomAD4 genome

AF:

0.00335

AC:

510

AN:

152386

Hom.:

Cov.:

AF XY:

0.00388

AC XY:

289

AN XY:

74514

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.000522

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.0205

Gnomad4 NFE

AF:

0.00378

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00277

Hom.:

Bravo

AF:

0.00165

TwinsUK

AF:

0.00135

AC:

ALSPAC

AF:

0.00234

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00349

AC:

ExAC

AF:

0.00325

AC:

394

EpiCase

AF:

0.00224

EpiControl

AF:

0.00291

ClinVar

Significance: Benign/Likely benign

Submissions summary: Pathogenic:2Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 05, 2023	- -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2024	NHERF1: BP4, BS1, BS2 -

Hypophosphatemic nephrolithiasis/osteoporosis 2

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Sep 11, 2008

- -

Hypophosphatemia;C0392525:Nephrolithiasis

Pathogenic:1

Likely pathogenic, no assertion criteria provided

literature only

Yale Center for Mendelian Genomics, Yale University

Sep 08, 2017

- -

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Gene has limited evidence for disease association. Variant reported in a patient with renal calcium lithiasis (Karim 2008), and one with Nephrolithiasis/Nephrocalcinosis (heterozygous, only variant in both cases. Gene is linlked to AD Nephrolithiasis) (Halbritter 2015). Frequency 2.2%. -

NHERF1-related disorder

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 08, 2020

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.27

BayesDel_noAF

Benign

-0.16

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.29

T;.

Eigen

Benign

-0.070

Eigen_PC

Benign

0.039

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.85

T;D

MetaRNN

Benign

0.0080

T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.0

N;.

PrimateAI

Benign

0.46

PROVEAN

Uncertain

-3.5

D;.

REVEL

Benign

0.20

Sift

Uncertain

0.0040

D;.

Sift4G

Uncertain

0.014

D;D

Polyphen

0.98

D;.

Vest4

0.61

MVP

0.26

MPC

0.33

ClinPred

0.046

GERP RS

4.5

Varity_R

0.79

gMVP

0.62

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over