rs2610739

Variant names:

• chr6-88543930-G-A
• rs2610739

Your query was ambiguous. Multiple possible variants found:

• chr6-88543930-G-A
• chr6-88543930-G-C
• chr6-88543930-G-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 0.858 in 152,240 control chromosomes in the GnomAD database, including 56,332 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 0.86 (56332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 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: 0.858 AC: 130498 AN: 152122 Hom.: 56285 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.858 AC: 130595 AN: 152240 Hom.: 56332 Cov.: 32 AF XY: 0.857 AC XY: 63800 AN XY: 74414

African (AFR) AF: 0.953 AC: 39575 AN: 41548

American (AMR) AF: 0.841 AC: 12862 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3041 AN: 3470

East Asian (EAS) AF: 0.896 AC: 4631 AN: 5170

South Asian (SAS) AF: 0.750 AC: 3616 AN: 4824

European-Finnish (FIN) AF: 0.838 AC: 8884 AN: 10604

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55207 AN: 68004

Other (OTH) AF: 0.844 AC: 1785 AN: 2116

Alfa AF: 0.838 Hom.: 90756

Bravo AF: 0.865

Asia WGS AF: 0.836 AC: 2905 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.6
DANN	Benign	0.35
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2610739; hg19: chr6-89253649;