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. The variant received -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

Our verdict: Benign. The variant received -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 AC: 0.87975 AN: 0.87975

Gnomad4 AMR AF: 0.867 AC: 0.866793 AN: 0.866793

Gnomad4 ASJ AF: 0.912 AC: 0.911578 AN: 0.911578

Gnomad4 EAS AF: 0.698 AC: 0.698339 AN: 0.698339

Gnomad4 SAS AF: 0.811 AC: 0.810816 AN: 0.810816

Gnomad4 FIN AF: 0.921 AC: 0.920596 AN: 0.920596

Gnomad4 NFE AF: 0.935 AC: 0.9346 AN: 0.9346

Gnomad4 OTH AF: 0.885 AC: 0.885052 AN: 0.885052

Alfa AF: 0.914 Hom.: 130385

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;