rs1357339

Variant names:

• chr11-81143332-C-A
• rs1357339

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.107 in 151,850 control chromosomes in the GnomAD database, including 1,164 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 0.11 (1164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) 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: 0.107 AC: 16268 AN: 151732 Hom.: 1162 Cov.: 32

Gnomad AFR AF: 0.0288

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0579

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.0992

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

GnomAD4 genome AF: 0.107 AC: 16265 AN: 151850 Hom.: 1164 Cov.: 32 AF XY: 0.105 AC XY: 7799 AN XY: 74220

Gnomad4 AFR AF: 0.0287

Gnomad4 AMR AF: 0.0912

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0579

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0890

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.0982

Alfa AF: 0.145 Hom.: 2518

Bravo AF: 0.101

Asia WGS AF: 0.137 AC: 478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.094
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1357339; hg19: chr11-80854375;