11-9565640-T-C

Position:

• chr11-9565640-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.590

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.683

Alfa AF: 0.710 Hom.: 37022

Bravo AF: 0.669

Asia WGS AF: 0.521 AC: 1813 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10770039; hg19: chr11-9587187;