rs11740860

Variant names:

• chr5-36852970-A-G
• rs11740860

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 0.116 in 152,248 control chromosomes in the GnomAD database, including 1,114 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 0.12 (1114 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.177 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: 0.116 AC: 17686 AN: 152128 Hom.: 1111 Cov.: 32

Gnomad AFR AF: 0.0987

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.116 AC: 17715 AN: 152248 Hom.: 1114 Cov.: 32 AF XY: 0.119 AC XY: 8857 AN XY: 74444

African (AFR) AF: 0.0988 AC: 4106 AN: 41544

American (AMR) AF: 0.183 AC: 2793 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 692 AN: 3470

East Asian (EAS) AF: 0.126 AC: 655 AN: 5186

South Asian (SAS) AF: 0.110 AC: 533 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10594

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7320 AN: 68026

Other (OTH) AF: 0.146 AC: 309 AN: 2110

Alfa AF: 0.114 Hom.: 119

Bravo AF: 0.121

Asia WGS AF: 0.162 AC: 561 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.1
DANN	Benign	0.65
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs11740860; hg19: chr5-36853072;