rs764637

Positions:

• chr2-210776279-G-A
• chr2-210776279-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.932 in 152,114 control chromosomes in the GnomAD database, including 66,050 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.93 (66050 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.932 AC: 141664 AN: 151996 Hom.: 66014 Cov.: 30

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.882

Gnomad AMR AF: 0.950

Gnomad ASJ AF: 0.922

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.903

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.934

Gnomad OTH AF: 0.923

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.932 AC: 141759 AN: 152114 Hom.: 66050 Cov.: 30 AF XY: 0.932 AC XY: 69281 AN XY: 74350

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.951

Gnomad4 ASJ AF: 0.922

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.903

Gnomad4 NFE AF: 0.934

Gnomad4 OTH AF: 0.924

Alfa AF: 0.930 Hom.: 56102

Bravo AF: 0.934

Asia WGS AF: 0.978 AC: 3402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
DANN	Benign	0.56

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs764637; hg19: chr2-211641003;