rs287354

Variant names:

• chr13-68665820-A-G
• rs287354

Your query was ambiguous. Multiple possible variants found:

• chr13-68665820-A-G
• chr13-68665820-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 0.606 in 151,804 control chromosomes in the GnomAD database, including 28,049 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 0.61 (28049 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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: 0.606 AC: 91955 AN: 151686 Hom.: 28007 Cov.: 31

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.606 AC: 92049 AN: 151804 Hom.: 28049 Cov.: 31 AF XY: 0.608 AC XY: 45092 AN XY: 74170

African (AFR) AF: 0.613 AC: 25381 AN: 41388

American (AMR) AF: 0.670 AC: 10190 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1960 AN: 3464

East Asian (EAS) AF: 0.687 AC: 3532 AN: 5138

South Asian (SAS) AF: 0.594 AC: 2858 AN: 4808

European-Finnish (FIN) AF: 0.641 AC: 6777 AN: 10572

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.578 AC: 39264 AN: 67922

Other (OTH) AF: 0.598 AC: 1264 AN: 2114

Alfa AF: 0.577 Hom.: 46030

Bravo AF: 0.607

Asia WGS AF: 0.661 AC: 2298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.084
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs287354; hg19: chr13-69239952;