rs11791649

Variant names:

• chr9-102085980-C-T
• rs11791649

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 0.296 in 151,632 control chromosomes in the GnomAD database, including 7,864 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 0.30 (7864 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 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: 0.297 AC: 44934 AN: 151512 Hom.: 7871 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.537

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.296 AC: 44925 AN: 151632 Hom.: 7864 Cov.: 31 AF XY: 0.296 AC XY: 21905 AN XY: 74038

African (AFR) AF: 0.139 AC: 5739 AN: 41360

American (AMR) AF: 0.265 AC: 4028 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1428 AN: 3466

East Asian (EAS) AF: 0.0694 AC: 357 AN: 5146

South Asian (SAS) AF: 0.309 AC: 1481 AN: 4796

European-Finnish (FIN) AF: 0.414 AC: 4337 AN: 10474

Middle Eastern (MID) AF: 0.479 AC: 138 AN: 288

European-Non Finnish (NFE) AF: 0.387 AC: 26261 AN: 67862

Other (OTH) AF: 0.317 AC: 666 AN: 2102

Alfa AF: 0.326 Hom.: 1272

Bravo AF: 0.277

Asia WGS AF: 0.169 AC: 585 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.92
DANN	Benign	0.61
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs11791649; hg19: chr9-104848262;