rs461404

Positions:

• chr5-40799438-G-A
• chr5-40799438-G-T

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 0.705 in 152,114 control chromosomes in the GnomAD database, including 37,793 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 0.70 (37793 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 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: 0.705 AC: 107119 AN: 151996 Hom.: 37759 Cov.: 34

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.705 AC: 107208 AN: 152114 Hom.: 37793 Cov.: 34 AF XY: 0.707 AC XY: 52619 AN XY: 74380

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.802

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.674

Alfa AF: 0.704 Hom.: 18910

Bravo AF: 0.707

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs461404; hg19: chr5-40799540;