2-207629510-T-C

Variant names:

• chr2-207629510-T-C
• rs2952768

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.351 in 151,972 control chromosomes in the GnomAD database, including 9,679 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 0.35 (9679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.737
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53308 AN: 151856 Hom.: 9659 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.351 AC: 53364 AN: 151972 Hom.: 9679 Cov.: 32 AF XY: 0.355 AC XY: 26365 AN XY: 74260

African (AFR) AF: 0.312 AC: 12926 AN: 41444

American (AMR) AF: 0.390 AC: 5955 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1011 AN: 3470

East Asian (EAS) AF: 0.388 AC: 2005 AN: 5168

South Asian (SAS) AF: 0.513 AC: 2471 AN: 4820

European-Finnish (FIN) AF: 0.383 AC: 4032 AN: 10526

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23859 AN: 67980

Other (OTH) AF: 0.332 AC: 699 AN: 2104

Alfa AF: 0.350 Hom.: 29474

Bravo AF: 0.352

Asia WGS AF: 0.439 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	10
DANN	Benign	0.53
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs2952768; hg19: chr2-208494234;