5-40410833-G-T

Variant names:

• chr5-40410833-G-T
• rs6451493

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 0.571 in 151,900 control chromosomes in the GnomAD database, including 25,485 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 0.57 (25485 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 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: 0.571 AC: 86694 AN: 151782 Hom.: 25470 Cov.: 32

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.571 AC: 86753 AN: 151900 Hom.: 25485 Cov.: 32 AF XY: 0.564 AC XY: 41844 AN XY: 74234

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.584

Alfa AF: 0.576 Hom.: 29323

Bravo AF: 0.564

Asia WGS AF: 0.373 AC: 1297 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6451493; hg19: chr5-40410935;