rs947990

Variant names:

• chr11-116686598-G-T
• rs947990

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 0.0866 in 152,032 control chromosomes in the GnomAD database, including 783 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 0.087 (783 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 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: 0.0867 AC: 13173 AN: 151914 Hom.: 784 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0735

Gnomad ASJ AF: 0.0819

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0814

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

GnomAD4 genome AF: 0.0866 AC: 13162 AN: 152032 Hom.: 783 Cov.: 32 AF XY: 0.0864 AC XY: 6421 AN XY: 74300

African (AFR) AF: 0.0233 AC: 968 AN: 41476

American (AMR) AF: 0.0734 AC: 1119 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0819 AC: 284 AN: 3466

East Asian (EAS) AF: 0.0517 AC: 268 AN: 5180

South Asian (SAS) AF: 0.114 AC: 546 AN: 4800

European-Finnish (FIN) AF: 0.106 AC: 1119 AN: 10556

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8633 AN: 67986

Other (OTH) AF: 0.0801 AC: 169 AN: 2110

Alfa AF: 0.112 Hom.: 1582

Bravo AF: 0.0785

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.73
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs947990; hg19: chr11-116557314;