rs4613763

Positions:

• chr5-40392626-T-C

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 0.14 in 152,124 control chromosomes in the GnomAD database, including 1,706 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 0.14 (1706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21224 AN: 152006 Hom.: 1701 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0732

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.140 AC: 21245 AN: 152124 Hom.: 1706 Cov.: 32 AF XY: 0.138 AC XY: 10257 AN XY: 74378

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.0858

Gnomad4 ASJ AF: 0.0732

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0174

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.111

Alfa AF: 0.124 Hom.: 2808

Bravo AF: 0.132

Asia WGS AF: 0.0280 AC: 98 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4613763; hg19: chr5-40392728;