rs9804646

chr11-116794363-C-T

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 0.173 in 152,074 control chromosomes in the GnomAD database, including 3,420 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 0.17 (3420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.345 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: 0.173 AC: 26233 AN: 151956 Hom.: 3420 Cov.: 32

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.173 AC: 26255 AN: 152074 Hom.: 3420 Cov.: 32 AF XY: 0.176 AC XY: 13075 AN XY: 74330

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.0815

Gnomad4 OTH AF: 0.142

Alfa AF: 0.115 Hom.: 319

Bravo AF: 0.179

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	4.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9804646; hg19: chr11-116665079; COSMIC: COSV57136635;