rs11650680

Variant names:

• chr17-40422984-C-T
• rs11650680

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 0.169 in 152,222 control chromosomes in the GnomAD database, including 2,685 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 0.17 (2685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.208 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: 0.169 AC: 25727 AN: 152104 Hom.: 2685 Cov.: 32

Gnomad AFR AF: 0.0415

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.169 AC: 25729 AN: 152222 Hom.: 2685 Cov.: 32 AF XY: 0.174 AC XY: 12964 AN XY: 74392

African (AFR) AF: 0.0414 AC: 1721 AN: 41566

American (AMR) AF: 0.212 AC: 3240 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 707 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1040 AN: 5172

South Asian (SAS) AF: 0.204 AC: 985 AN: 4828

European-Finnish (FIN) AF: 0.289 AC: 3059 AN: 10568

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14375 AN: 68018

Other (OTH) AF: 0.195 AC: 411 AN: 2112

Alfa AF: 0.174 Hom.: 2121

Bravo AF: 0.157

Asia WGS AF: 0.220 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.60
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs11650680; hg19: chr17-38579236;