rs11602918

Variant names:

• chr11-130615624-T-C
• rs11602918

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 0.132 in 152,196 control chromosomes in the GnomAD database, including 1,709 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 0.13 (1709 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.446
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.187 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: 0.132 AC: 20066 AN: 152078 Hom.: 1711 Cov.: 33

Gnomad AFR AF: 0.0347

Gnomad AMI AF: 0.194

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00463

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.132 AC: 20058 AN: 152196 Hom.: 1709 Cov.: 33 AF XY: 0.132 AC XY: 9804 AN XY: 74392

African (AFR) AF: 0.0346 AC: 1438 AN: 41554

American (AMR) AF: 0.140 AC: 2148 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3468

East Asian (EAS) AF: 0.00483 AC: 25 AN: 5176

South Asian (SAS) AF: 0.117 AC: 562 AN: 4820

European-Finnish (FIN) AF: 0.191 AC: 2016 AN: 10574

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12890 AN: 67990

Other (OTH) AF: 0.142 AC: 300 AN: 2112

Alfa AF: 0.151 Hom.: 377

Bravo AF: 0.125

Asia WGS AF: 0.0620 AC: 215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs11602918; hg19: chr11-130485519;