2-102470310-A-C

Variant names:

• chr2-102470310-A-C
• rs990171

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 0.777 in 152,106 control chromosomes in the GnomAD database, including 46,902 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 0.78 (46902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118033 AN: 151988 Hom.: 46859 Cov.: 32

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.777 AC: 118125 AN: 152106 Hom.: 46902 Cov.: 32 AF XY: 0.771 AC XY: 57305 AN XY: 74340

African (AFR) AF: 0.902 AC: 37468 AN: 41536

American (AMR) AF: 0.605 AC: 9230 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2659 AN: 3466

East Asian (EAS) AF: 0.552 AC: 2848 AN: 5160

South Asian (SAS) AF: 0.560 AC: 2699 AN: 4818

European-Finnish (FIN) AF: 0.812 AC: 8576 AN: 10568

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.767 AC: 52150 AN: 67974

Other (OTH) AF: 0.757 AC: 1599 AN: 2112

Alfa AF: 0.742 Hom.: 9808

Bravo AF: 0.766

Asia WGS AF: 0.579 AC: 2016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.80
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs990171; hg19: chr2-103086770; COSMIC: COSV54830565;