11-9565640-T-C

Variant names:

• chr11-9565640-T-C
• rs10770039

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 0.667 in 152,100 control chromosomes in the GnomAD database, including 34,228 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 0.67 (34228 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101369 AN: 151982 Hom.: 34222 Cov.: 32

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.667 AC: 101410 AN: 152100 Hom.: 34228 Cov.: 32 AF XY: 0.660 AC XY: 49102 AN XY: 74348

African (AFR) AF: 0.607 AC: 25169 AN: 41472

American (AMR) AF: 0.684 AC: 10445 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2231 AN: 3472

East Asian (EAS) AF: 0.461 AC: 2387 AN: 5174

South Asian (SAS) AF: 0.590 AC: 2845 AN: 4822

European-Finnish (FIN) AF: 0.681 AC: 7201 AN: 10572

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.718 AC: 48812 AN: 67986

Other (OTH) AF: 0.683 AC: 1446 AN: 2116

Alfa AF: 0.708 Hom.: 44513

Bravo AF: 0.669

Asia WGS AF: 0.521 AC: 1813 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.16
DANN	Benign	0.58
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10770039; hg19: chr11-9587187;