rs2817953

Variant names:

• chr6-120865640-G-A
• rs2817953

Your query was ambiguous. Multiple possible variants found:

• chr6-120865640-G-A
• chr6-120865640-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 0.441 in 151,320 control chromosomes in the GnomAD database, including 17,378 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 0.44 (17378 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.498
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.678 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: 0.440 AC: 66548 AN: 151200 Hom.: 17329 Cov.: 32

Gnomad AFR AF: 0.685

Gnomad AMI AF: 0.183

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.441 AC: 66662 AN: 151320 Hom.: 17378 Cov.: 32 AF XY: 0.442 AC XY: 32648 AN XY: 73946

African (AFR) AF: 0.685 AC: 28337 AN: 41366

American (AMR) AF: 0.562 AC: 8518 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1320 AN: 3454

East Asian (EAS) AF: 0.604 AC: 3121 AN: 5170

South Asian (SAS) AF: 0.528 AC: 2545 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2137 AN: 10546

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19477 AN: 67486

Other (OTH) AF: 0.434 AC: 912 AN: 2100

Alfa AF: 0.184 Hom.: 319

Bravo AF: 0.477

Asia WGS AF: 0.585 AC: 2028 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.13
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2817953; hg19: chr6-121186786;