rs13140875

Variant names:

• chr4-167936311-T-C
• rs13140875

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 0.118 in 152,248 control chromosomes in the GnomAD database, including 1,186 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 (1186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 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: 0.118 AC: 17919 AN: 152130 Hom.: 1181 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0796

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0655

Gnomad FIN AF: 0.0849

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.118 AC: 17951 AN: 152248 Hom.: 1186 Cov.: 32 AF XY: 0.113 AC XY: 8435 AN XY: 74458

African (AFR) AF: 0.147 AC: 6123 AN: 41540

American (AMR) AF: 0.0793 AC: 1213 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 341 AN: 3472

East Asian (EAS) AF: 0.00328 AC: 17 AN: 5186

South Asian (SAS) AF: 0.0658 AC: 317 AN: 4820

European-Finnish (FIN) AF: 0.0849 AC: 901 AN: 10614

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.127 AC: 8604 AN: 68002

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.124 Hom.: 1952

Bravo AF: 0.119

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.4
DANN	Benign	0.53
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs13140875; hg19: chr4-168857462;