rs13140817

Variant names:

• chr4-9761351-G-A
• rs13140817

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 0.545 in 151,996 control chromosomes in the GnomAD database, including 23,632 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 0.54 (23632 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.635 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: 0.545 AC: 82743 AN: 151878 Hom.: 23620 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.545 AC: 82777 AN: 151996 Hom.: 23632 Cov.: 31 AF XY: 0.542 AC XY: 40230 AN XY: 74288

African (AFR) AF: 0.393 AC: 16276 AN: 41460

American (AMR) AF: 0.551 AC: 8412 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2473 AN: 3468

East Asian (EAS) AF: 0.329 AC: 1691 AN: 5144

South Asian (SAS) AF: 0.463 AC: 2228 AN: 4814

European-Finnish (FIN) AF: 0.601 AC: 6353 AN: 10568

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43524 AN: 67964

Other (OTH) AF: 0.546 AC: 1151 AN: 2108

Alfa AF: 0.603 Hom.: 36730

Bravo AF: 0.536

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.75
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs13140817; hg19: chr4-9762975;