rs2687855

Variant names:

• chr3-145768292-G-A
• rs2687855

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 0.699 in 151,788 control chromosomes in the GnomAD database, including 38,404 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 0.70 (38404 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 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: 0.699 AC: 106038 AN: 151670 Hom.: 38355 Cov.: 31

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.699 AC: 106134 AN: 151788 Hom.: 38404 Cov.: 31 AF XY: 0.695 AC XY: 51531 AN XY: 74134

African (AFR) AF: 0.870 AC: 36106 AN: 41492

American (AMR) AF: 0.575 AC: 8742 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2352 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1627 AN: 5130

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4816

European-Finnish (FIN) AF: 0.711 AC: 7501 AN: 10554

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45008 AN: 67810

Other (OTH) AF: 0.705 AC: 1483 AN: 2104

Alfa AF: 0.711 Hom.: 5549

Bravo AF: 0.697

Asia WGS AF: 0.503 AC: 1754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.74
DANN	Benign	0.33
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2687855; hg19: chr3-145486079;