Variant 1-42830851-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_001017922.2(ERMAP):c.169G>A(p.Gly57Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00271 in 1,607,760 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0018 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0028 ( 8 hom. )

Consequence

ERMAP
NM_001017922.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter P:1B:1

Conservation

PhyloP100: 0.434

Variant links:

Genes affected

ERMAP (HGNC:15743): (erythroblast membrane associated protein (Scianna blood group)) The protein encoded by this gene is a cell surface transmembrane protein that may act as an erythroid cell receptor, possibly as a mediator of cell adhesion. Polymorphisms in this gene are responsible for the Scianna/Radin blood group system. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ERMAP links:

ERMAP (HGNC:):

ERMAP links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.04339391).

BP6

Variant 1-42830851-G-A is Benign according to our data. Variant chr1-42830851-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1916.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-42830851-G-A is described in Lovd as [Likely_benign].

BS2

High Homozygotes in GnomAdExome4 at 8 BG gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ERMAP	NM_001017922.2 linkuse as main transcript	c.169G>A	p.Gly57Arg	missense_variant	4/12	ENST00000372517.8	NP_001017922.1	Q96PL5A0A1C9HIH9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ERMAP	ENST00000372517.8 linkuse as main transcript	c.169G>A	p.Gly57Arg	missense_variant	4/12	1	NM_001017922.2	ENSP00000361595.2		Q96PL5

Frequencies

GnomAD3 genomes

AF:

0.00184

AC:

280

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000410

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00170

Gnomad ASJ

AF:

0.00404

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00124

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00309

Gnomad OTH

AF:

0.00143

GnomAD3 exomes

AF:

0.00189

AC:

451

AN:

238326

Hom.:

AF XY:

0.00200

AC XY:

257

AN XY:

128738

show subpopulations

Gnomad AFR exome

AF:

0.000334

Gnomad AMR exome

AF:

0.000935

Gnomad ASJ exome

AF:

0.00296

Gnomad EAS exome

AF:

0.000172

Gnomad SAS exome

AF:

0.00133

Gnomad FIN exome

AF:

0.000147

Gnomad NFE exome

AF:

0.00307

Gnomad OTH exome

AF:

0.00204

GnomAD4 exome

AF:

0.00280

AC:

4073

AN:

1455454

Hom.:

Cov.:

AF XY:

0.00280

AC XY:

2026

AN XY:

723540

show subpopulations

Gnomad4 AFR exome

AF:

0.000240

Gnomad4 AMR exome

AF:

0.00101

Gnomad4 ASJ exome

AF:

0.00262

Gnomad4 EAS exome

AF:

0.000280

Gnomad4 SAS exome

AF:

0.000938

Gnomad4 FIN exome

AF:

0.000264

Gnomad4 NFE exome

AF:

0.00333

Gnomad4 OTH exome

AF:

0.00228

GnomAD4 genome

AF:

0.00184

AC:

280

AN:

152306

Hom.:

Cov.:

AF XY:

0.00187

AC XY:

139

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.000409

Gnomad4 AMR

AF:

0.00170

Gnomad4 ASJ

AF:

0.00404

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00124

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00309

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00301

Hom.:

Bravo

AF:

0.00177

TwinsUK

AF:

0.00108

AC:

ALSPAC

AF:

0.00285

AC:

ESP6500AA

AF:

0.000227

AC:

ESP6500EA

AF:

0.00302

AC:

ExAC

AF:

0.00181

AC:

220

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Pathogenic:1Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

SCIANNA BLOOD GROUP SYSTEM, SC:-1,2

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 15, 2003

- -

not specified

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Genomic Research Center, Shahid Beheshti University of Medical Sciences

Jan 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.51

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Benign

0.74

DEOGEN2

Benign

0.0024

T;T

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.78

FATHMM_MKL

Benign

0.047

LIST_S2

Benign

0.63

.;T

M_CAP

Benign

0.0085

MetaRNN

Benign

0.043

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.94

L;L

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.63

N;N

REVEL

Benign

0.040

Sift

Benign

0.15

T;T

Sift4G

Benign

0.21

T;T

Polyphen

0.51

P;P

Vest4

0.23

MutPred

0.55

Gain of MoRF binding (P = 0.0072);Gain of MoRF binding (P = 0.0072);

MVP

0.32

MPC

0.21

ClinPred

0.0064

GERP RS

1.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.12

gMVP

0.45

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