rs13140817

Positions:

• chr4-9761351-G-A

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 0.545 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.9761351G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.546

Alfa AF: 0.577 Hom.: 3371

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13140817; hg19: chr4-9762975;