rs11157317

Variant names:

• chr14-42934256-C-T
• rs11157317

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 0.255 in 151,554 control chromosomes in the GnomAD database, including 5,169 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 0.25 (5169 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.362 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: 0.255 AC: 38561 AN: 151436 Hom.: 5164 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.255 AC: 38587 AN: 151554 Hom.: 5169 Cov.: 31 AF XY: 0.255 AC XY: 18851 AN XY: 74014

African (AFR) AF: 0.222 AC: 9187 AN: 41412

American (AMR) AF: 0.370 AC: 5594 AN: 15128

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 543 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1747 AN: 5142

South Asian (SAS) AF: 0.214 AC: 1030 AN: 4810

European-Finnish (FIN) AF: 0.206 AC: 2167 AN: 10498

Middle Eastern (MID) AF: 0.164 AC: 48 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17463 AN: 67782

Other (OTH) AF: 0.234 AC: 494 AN: 2108

Alfa AF: 0.255 Hom.: 15380

Bravo AF: 0.270

Asia WGS AF: 0.239 AC: 826 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.83
DANN	Benign	0.25
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs11157317; hg19: chr14-43403459;