Variant 17-81438420-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001377448.1(BAHCC1):c.409G>A(p.Val137Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00577 in 778,454 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0051 ( 4 hom., cov: 33)

Exomes 𝑓: 0.0059 ( 16 hom. )

Consequence

BAHCC1
NM_001377448.1 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.29

Variant links:

Genes affected

BAHCC1 (HGNC:29279): (BAH domain and coiled-coil containing 1) Predicted to enable chromatin binding activity. [provided by Alliance of Genome Resources, Apr 2022]

BAHCC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0061863363).

BP6

Variant 17-81438420-G-A is Benign according to our data. Variant chr17-81438420-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2648447.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd at 4 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BAHCC1	NM_001377448.1 linkuse as main transcript	c.409G>A	p.Val137Met	missense_variant	4/28	ENST00000675386.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BAHCC1	ENST00000675386.2 linkuse as main transcript	c.409G>A	p.Val137Met	missense_variant	4/28		NM_001377448.1	P2
BAHCC1	ENST00000584436.7 linkuse as main transcript	c.409G>A	p.Val137Met	missense_variant	4/29	5		A2

Frequencies

GnomAD3 genomes

AF:

0.00509

AC:

774

AN:

152126

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00121

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00464

Gnomad ASJ

AF:

0.0104

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00310

Gnomad FIN

AF:

0.00848

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00721

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.00540

AC:

1320

AN:

244510

Hom.:

AF XY:

0.00548

AC XY:

730

AN XY:

133220

show subpopulations

Gnomad AFR exome

AF:

0.00123

Gnomad AMR exome

AF:

0.00258

Gnomad ASJ exome

AF:

0.00963

Gnomad EAS exome

AF:

0.000224

Gnomad SAS exome

AF:

0.00312

Gnomad FIN exome

AF:

0.0106

Gnomad NFE exome

AF:

0.00682

Gnomad OTH exome

AF:

0.00705

GnomAD4 exome

AF:

0.00594

AC:

3717

AN:

626210

Hom.:

Cov.:

AF XY:

0.00593

AC XY:

2023

AN XY:

341048

show subpopulations

Gnomad4 AFR exome

AF:

0.00113

Gnomad4 AMR exome

AF:

0.00267

Gnomad4 ASJ exome

AF:

0.00875

Gnomad4 EAS exome

AF:

0.000111

Gnomad4 SAS exome

AF:

0.00317

Gnomad4 FIN exome

AF:

0.0101

Gnomad4 NFE exome

AF:

0.00696

Gnomad4 OTH exome

AF:

0.00545

GnomAD4 genome

AF:

0.00507

AC:

772

AN:

152244

Hom.:

Cov.:

AF XY:

0.00497

AC XY:

370

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.00120

Gnomad4 AMR

AF:

0.00464

Gnomad4 ASJ

AF:

0.0104

Gnomad4 EAS

AF:

0.000194

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00848

Gnomad4 NFE

AF:

0.00721

Gnomad4 OTH

AF:

0.00662

Alfa

AF:

0.00597

Hom.:

Bravo

AF:

0.00440

TwinsUK

AF:

0.00620

AC:

ALSPAC

AF:

0.00986

AC:

ESP6500AA

AF:

0.00198

AC:

ESP6500EA

AF:

0.00718

AC:

ExAC

AF:

0.00483

AC:

581

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00802

EpiControl

AF:

0.00715

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

BAHCC1: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.60

Cadd

Benign

Dann

Benign

0.14

DEOGEN2

Benign

0.078

T;T

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.38

FATHMM_MKL

Benign

0.33

LIST_S2

Benign

0.84

T;D

MetaRNN

Benign

0.0062

T;T

MetaSVM

Benign

-0.94

MutationAssessor

Benign

-0.76

N;.

MutationTaster

Benign

0.84

PrimateAI

Benign

0.37

Sift4G

Benign

1.0

T;T

Polyphen

0.0020

B;.

Vest4

0.31

MVP

0.014

MPC

0.087

ClinPred

0.0073

GERP RS

2.8

Varity_R

0.034

gMVP

0.20

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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