Variant chr2-126695903-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002101.5(GYPC):c.191-43G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 1,541,388 control chromosomes in the GnomAD database, including 44,526 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6632 hom., cov: 33)

Exomes 𝑓: 0.23 ( 37894 hom. )

Consequence

GYPC
NM_002101.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.619

Variant links:

Genes affected

GYPC (HGNC:4704): (glycophorin C (Gerbich blood group)) Glycophorin C (GYPC) is an integral membrane glycoprotein. It is a minor species carried by human erythrocytes, but plays an important role in regulating the mechanical stability of red cells. A number of glycophorin C mutations have been described. The Gerbich and Yus phenotypes are due to deletion of exon 3 and 2, respectively. The Webb and Duch antigens, also known as glycophorin D, result from single point mutations of the glycophorin C gene. The glycophorin C protein has very little homology with glycophorins A and B. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

GYPC links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 2-126695903-G-A is Benign according to our data. Variant chr2-126695903-G-A is described in ClinVar as [Benign]. Clinvar id is 1258136.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GYPC	NM_002101.5 linkuse as main transcript	c.191-43G>A		intron_variant		ENST00000259254.9	NP_002092.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
GYPC	ENST00000259254.9 linkuse as main transcript	c.191-43G>A	intron_variant	1	NM_002101.5	ENSP00000259254	P2	P04921-1
GYPC	ENST00000356887.12 linkuse as main transcript	c.128-43G>A	intron_variant	1		ENSP00000349354	A2	P04921-2
GYPC	ENST00000409836.3 linkuse as main transcript	c.134-43G>A	intron_variant	1		ENSP00000386904	A2	P04921-3

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42382

AN:

151932

Hom.:

6618

Cov.:

show subpopulations

Gnomad AFR

AF:

0.404

Gnomad AMI

AF:

0.230

Gnomad AMR

AF:

0.302

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.415

Gnomad SAS

AF:

0.157

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.281

GnomAD3 exomes

AF:

0.248

AC:

61770

AN:

249060

Hom.:

8504

AF XY:

0.237

AC XY:

31985

AN XY:

134784

show subpopulations

Gnomad AFR exome

AF:

0.411

Gnomad AMR exome

AF:

0.317

Gnomad ASJ exome

AF:

0.186

Gnomad EAS exome

AF:

0.423

Gnomad SAS exome

AF:

0.145

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.220

Gnomad OTH exome

AF:

0.227

GnomAD4 exome

AF:

0.227

AC:

315186

AN:

1389338

Hom.:

37894

Cov.:

AF XY:

0.222

AC XY:

154601

AN XY:

695612

show subpopulations

Gnomad4 AFR exome

AF:

0.420

Gnomad4 AMR exome

AF:

0.318

Gnomad4 ASJ exome

AF:

0.189

Gnomad4 EAS exome

AF:

0.348

Gnomad4 SAS exome

AF:

0.150

Gnomad4 FIN exome

AF:

0.195

Gnomad4 NFE exome

AF:

0.221

Gnomad4 OTH exome

AF:

0.235

GnomAD4 genome

AF:

0.279

AC:

42441

AN:

152050

Hom.:

6632

Cov.:

AF XY:

0.279

AC XY:

20769

AN XY:

74328

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.301

Gnomad4 ASJ

AF:

0.181

Gnomad4 EAS

AF:

0.414

Gnomad4 SAS

AF:

0.158

Gnomad4 FIN

AF:

0.193

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.278

Alfa

AF:

0.242

Hom.:

1020

Bravo

AF:

0.300

Asia WGS

AF:

0.253

AC:

878

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.88

DANN

Benign

0.55

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