rs11791649

Variant names:

• chr9-102085980-C-T
• rs11791649

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 0.296 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.0694

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.317

Alfa AF: 0.333 Hom.: 1259

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11791649; hg19: chr9-104848262;