rs11167814

Variant names:

• chr5-143477939-C-G
• rs11167814

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 0.287 in 152,042 control chromosomes in the GnomAD database, including 6,407 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 0.29 (6407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• 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 (AFR) allele frequency at 95% confidence interval = 0.29 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: 0.287 AC: 43582 AN: 151924 Hom.: 6402 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.287 AC: 43605 AN: 152042 Hom.: 6407 Cov.: 32 AF XY: 0.288 AC XY: 21358 AN XY: 74284

African (AFR) AF: 0.294 AC: 12205 AN: 41456

American (AMR) AF: 0.253 AC: 3864 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3472

East Asian (EAS) AF: 0.278 AC: 1442 AN: 5186

South Asian (SAS) AF: 0.238 AC: 1146 AN: 4820

European-Finnish (FIN) AF: 0.292 AC: 3082 AN: 10542

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19597 AN: 67982

Other (OTH) AF: 0.310 AC: 650 AN: 2100

Alfa AF: 0.289 Hom.: 822

Bravo AF: 0.284

Asia WGS AF: 0.303 AC: 1052 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	1.4
DANN	Benign	0.52
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs11167814; hg19: chr5-142857504; COSMIC: COSV60203176;