11-119349302-G-C

Variant names:

• chr11-119349302-G-C
• rs7932692

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 0.589 in 151,798 control chromosomes in the GnomAD database, including 26,507 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 0.59 (26507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.719 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: 0.589 AC: 89372 AN: 151680 Hom.: 26476 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.707

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.589 AC: 89451 AN: 151798 Hom.: 26507 Cov.: 32 AF XY: 0.591 AC XY: 43809 AN XY: 74166

African (AFR) AF: 0.579 AC: 23966 AN: 41374

American (AMR) AF: 0.553 AC: 8427 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1990 AN: 3464

East Asian (EAS) AF: 0.739 AC: 3819 AN: 5168

South Asian (SAS) AF: 0.678 AC: 3263 AN: 4812

European-Finnish (FIN) AF: 0.547 AC: 5748 AN: 10510

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.590 AC: 40094 AN: 67920

Other (OTH) AF: 0.609 AC: 1286 AN: 2110

Alfa AF: 0.450 Hom.: 1165

Bravo AF: 0.593

Asia WGS AF: 0.717 AC: 2493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.37
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7932692; hg19: chr11-119220012;