rs6739015

Variant names:

• chr2-85528234-A-G
• rs6739015

Your query was ambiguous. Multiple possible variants found:

• chr2-85528234-A-G
• chr2-85528234-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 0.493 in 151,974 control chromosomes in the GnomAD database, including 19,778 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 0.49 (19778 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721
• Publications: 30 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74844 AN: 151856 Hom.: 19748 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.493 AC: 74930 AN: 151974 Hom.: 19778 Cov.: 32 AF XY: 0.489 AC XY: 36370 AN XY: 74306

African (AFR) AF: 0.695 AC: 28803 AN: 41444

American (AMR) AF: 0.394 AC: 6010 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2006 AN: 5152

South Asian (SAS) AF: 0.385 AC: 1856 AN: 4824

European-Finnish (FIN) AF: 0.440 AC: 4652 AN: 10562

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28840 AN: 67942

Other (OTH) AF: 0.472 AC: 996 AN: 2112

Alfa AF: 0.440 Hom.: 58335

Bravo AF: 0.498

Asia WGS AF: 0.434 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.71
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs6739015; hg19: chr2-85755357;