Variant chr2-126690187-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.50-68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 1,147,440 control chromosomes in the GnomAD database, including 181,664 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.59 ( 27144 hom., cov: 33)

Exomes 𝑓: 0.55 ( 154520 hom. )

Consequence

GYPC
NM_002101.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.34

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=-0.89).

BP6

Variant 2-126690187-G-A is Benign according to our data. Variant chr2-126690187-G-A is described in ClinVar as [Benign]. Clinvar id is 1257983.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 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.50-68G>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.50-68G>A	intron_variant	1	NM_002101.5	ENSP00000259254	P2	P04921-1
GYPC	ENST00000356887.12 linkuse as main transcript	c.-14-68G>A	intron_variant	1		ENSP00000349354	A2	P04921-2
GYPC	ENST00000409836.3 linkuse as main transcript	c.50-3677G>A	intron_variant	1		ENSP00000386904	A2	P04921-3

Frequencies

GnomAD3 genomes

AF:

0.592

AC:

90032

AN:

151960

Hom.:

27108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.697

Gnomad AMI

AF:

0.529

Gnomad AMR

AF:

0.544

Gnomad ASJ

AF:

0.536

Gnomad EAS

AF:

0.652

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.559

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.554

Gnomad OTH

AF:

0.606

GnomAD4 exome

AF:

0.554

AC:

551251

AN:

995362

Hom.:

154520

AF XY:

0.548

AC XY:

282766

AN XY:

515610

show subpopulations

Gnomad4 AFR exome

AF:

0.706

Gnomad4 AMR exome

AF:

0.489

Gnomad4 ASJ exome

AF:

0.547

Gnomad4 EAS exome

AF:

0.605

Gnomad4 SAS exome

AF:

0.446

Gnomad4 FIN exome

AF:

0.551

Gnomad4 NFE exome

AF:

0.561

Gnomad4 OTH exome

AF:

0.566

GnomAD4 genome

AF:

0.593

AC:

90122

AN:

152078

Hom.:

27144

Cov.:

AF XY:

0.591

AC XY:

43942

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.697

Gnomad4 AMR

AF:

0.543

Gnomad4 ASJ

AF:

0.536

Gnomad4 EAS

AF:

0.653

Gnomad4 SAS

AF:

0.458

Gnomad4 FIN

AF:

0.559

Gnomad4 NFE

AF:

0.554

Gnomad4 OTH

AF:

0.604

Alfa

AF:

0.431

Hom.:

1148

Bravo

AF:

0.602

Asia WGS

AF:

0.532

AC:

1849

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

-0.89

CADD

Benign

0.049

DANN

Benign

0.73

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