rs9586708

Variant names:

• chr13-105064056-G-A
• rs9586708

Your query was ambiguous. Multiple possible variants found:

• chr13-105064056-G-A
• chr13-105064056-G-C
• chr13-105064056-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 0.657 in 152,040 control chromosomes in the GnomAD database, including 33,534 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 0.66 (33534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.911 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: 0.657 AC: 99876 AN: 151922 Hom.: 33505 Cov.: 32

Gnomad AFR AF: 0.758

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.643

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.657 AC: 99946 AN: 152040 Hom.: 33534 Cov.: 32 AF XY: 0.662 AC XY: 49179 AN XY: 74322

African (AFR) AF: 0.758 AC: 31406 AN: 41446

American (AMR) AF: 0.526 AC: 8038 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2175 AN: 3472

East Asian (EAS) AF: 0.933 AC: 4828 AN: 5176

South Asian (SAS) AF: 0.763 AC: 3683 AN: 4824

European-Finnish (FIN) AF: 0.662 AC: 6995 AN: 10566

Middle Eastern (MID) AF: 0.640 AC: 187 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40551 AN: 67966

Other (OTH) AF: 0.647 AC: 1366 AN: 2112

Alfa AF: 0.620 Hom.: 14907

Bravo AF: 0.651

Asia WGS AF: 0.825 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.76
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs9586708; hg19: chr13-105716407;