rs2651458

Variant names:

• chr8-96613222-A-C
• rs2651458

Your query was ambiguous. Multiple possible variants found:

• chr8-96613222-A-C
• chr8-96613222-A-T

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 0.586 in 152,126 control chromosomes in the GnomAD database, including 29,948 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 0.59 (29948 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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: 0.586 AC: 89074 AN: 152008 Hom.: 29960 Cov.: 33

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.586 AC: 89076 AN: 152126 Hom.: 29948 Cov.: 33 AF XY: 0.582 AC XY: 43232 AN XY: 74342

African (AFR) AF: 0.254 AC: 10559 AN: 41494

American (AMR) AF: 0.625 AC: 9557 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2556 AN: 3472

East Asian (EAS) AF: 0.346 AC: 1785 AN: 5166

South Asian (SAS) AF: 0.543 AC: 2623 AN: 4828

European-Finnish (FIN) AF: 0.711 AC: 7521 AN: 10580

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52375 AN: 67992

Other (OTH) AF: 0.603 AC: 1272 AN: 2108

Alfa AF: 0.714 Hom.: 169442

Bravo AF: 0.569

Asia WGS AF: 0.429 AC: 1492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.39
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs2651458; hg19: chr8-97625450;