rs660647

Variant names:

• chr11-106288424-A-G
• rs660647

Your query was ambiguous. Multiple possible variants found:

• chr11-106288424-A-G
• chr11-106288424-A-T

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 0.158 in 152,244 control chromosomes in the GnomAD database, including 2,135 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 0.16 (2135 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.768
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 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: 0.158 AC: 24020 AN: 152126 Hom.: 2127 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.158 AC: 24054 AN: 152244 Hom.: 2135 Cov.: 33 AF XY: 0.156 AC XY: 11648 AN XY: 74450

African (AFR) AF: 0.216 AC: 8953 AN: 41530

American (AMR) AF: 0.166 AC: 2538 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3470

East Asian (EAS) AF: 0.331 AC: 1716 AN: 5186

South Asian (SAS) AF: 0.159 AC: 768 AN: 4826

European-Finnish (FIN) AF: 0.0704 AC: 748 AN: 10622

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.118 AC: 8014 AN: 67996

Other (OTH) AF: 0.182 AC: 384 AN: 2112

Alfa AF: 0.117 Hom.: 710

Bravo AF: 0.169

Asia WGS AF: 0.252 AC: 878 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.77
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs660647; hg19: chr11-106159151;