rs662799

Variant names:

• chr11-116792991-G-A
• rs662799

Your query was ambiguous. Multiple possible variants found:

• chr11-116792991-G-A
• chr11-116792991-G-C

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 0.899 in 152,224 control chromosomes in the GnomAD database, including 61,676 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 0.90 (61676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.929 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: 0.899 AC: 136711 AN: 152106 Hom.: 61657 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.899 AC: 136785 AN: 152224 Hom.: 61676 Cov.: 32 AF XY: 0.895 AC XY: 66601 AN XY: 74420

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.811

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.935

Gnomad4 OTH AF: 0.885

Alfa AF: 0.913 Hom.: 23370

Bravo AF: 0.894

Asia WGS AF: 0.767 AC: 2668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs662799; hg19: chr11-116663707;