rs10758669

Variant names:

• chr9-4981602-C-A
• rs10758669

Your query was ambiguous. Multiple possible variants found:

• chr9-4981602-C-A
• chr9-4981602-C-G
• chr9-4981602-C-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 0.691 in 152,010 control chromosomes in the GnomAD database, including 36,980 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 0.69 (36980 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 140 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.821 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: 0.691 AC: 104991 AN: 151892 Hom.: 36947 Cov.: 32

Gnomad AFR AF: 0.829

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.691 AC: 105089 AN: 152010 Hom.: 36980 Cov.: 32 AF XY: 0.687 AC XY: 51043 AN XY: 74296

African (AFR) AF: 0.829 AC: 34383 AN: 41488

American (AMR) AF: 0.604 AC: 9227 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2187 AN: 3472

East Asian (EAS) AF: 0.639 AC: 3302 AN: 5168

South Asian (SAS) AF: 0.583 AC: 2802 AN: 4804

European-Finnish (FIN) AF: 0.639 AC: 6729 AN: 10536

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.653 AC: 44405 AN: 67952

Other (OTH) AF: 0.667 AC: 1408 AN: 2112

Alfa AF: 0.660 Hom.: 139271

Bravo AF: 0.699

Asia WGS AF: 0.605 AC: 2107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.59
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10758669; hg19: chr9-4981602;