rs11792644

Variant names:

• chr9-119796312-T-A
• rs11792644

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 0.0534 in 152,182 control chromosomes in the GnomAD database, including 296 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 0.053 (296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0809 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: 0.0534 AC: 8120 AN: 152064 Hom.: 296 Cov.: 32

Gnomad AFR AF: 0.0149

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0448

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0534 AC: 8121 AN: 152182 Hom.: 296 Cov.: 32 AF XY: 0.0520 AC XY: 3866 AN XY: 74386

Gnomad4 AFR AF: 0.0149

Gnomad4 AMR AF: 0.0419

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0456

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0827

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0620 Hom.: 47

Bravo AF: 0.0500

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.5
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11792644; hg19: chr9-122558590;