Variant chr2-126695810-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002101.5(GYPC):c.191-136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 745,320 control chromosomes in the GnomAD database, including 23,247 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6645 hom., cov: 33)

Exomes 𝑓: 0.23 ( 16602 hom. )

Consequence

GYPC
NM_002101.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.689

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 -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 2-126695810-C-T is Benign according to our data. Variant chr2-126695810-C-T is described in ClinVar as [Benign]. Clinvar id is 1238066.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GYPC	NM_002101.5 linkuse as main transcript	c.191-136C>T		intron_variant		ENST00000259254.9

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
GYPC	ENST00000259254.9 linkuse as main transcript	c.191-136C>T	intron_variant	1	NM_002101.5	P2	P04921-1
GYPC	ENST00000356887.12 linkuse as main transcript	c.128-136C>T	intron_variant	1		A2	P04921-2
GYPC	ENST00000409836.3 linkuse as main transcript	c.134-136C>T	intron_variant	1		A2	P04921-3

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42431

AN:

152022

Hom.:

6631

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:

0.416

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.281

GnomAD4 exome

AF:

0.228

AC:

134951

AN:

593180

Hom.:

16602

AF XY:

0.219

AC XY:

70250

AN XY:

320124

show subpopulations

Gnomad4 AFR exome

AF:

0.415

Gnomad4 AMR exome

AF:

0.316

Gnomad4 ASJ exome

AF:

0.189

Gnomad4 EAS exome

AF:

0.340

Gnomad4 SAS exome

AF:

0.149

Gnomad4 FIN exome

AF:

0.196

Gnomad4 NFE exome

AF:

0.218

Gnomad4 OTH exome

AF:

0.239

GnomAD4 genome

AF:

0.279

AC:

42490

AN:

152140

Hom.:

6645

Cov.:

AF XY:

0.280

AC XY:

20803

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.404

Gnomad4 AMR

AF:

0.301

Gnomad4 ASJ

AF:

0.181

Gnomad4 EAS

AF:

0.416

Gnomad4 SAS

AF:

0.157

Gnomad4 FIN

AF:

0.193

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.278

Alfa

AF:

0.258

Hom.:

870

Bravo

AF:

0.300

Asia WGS

AF:

0.253

AC:

878

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

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

-0.93

CADD

Benign

1.1

DANN

Benign

0.14

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