rs261137

Positions:

• chr5-4361007-C-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 0.516 in 151,976 control chromosomes in the GnomAD database, including 21,046 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 0.52 (21046 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 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: 0.516 AC: 78379 AN: 151858 Hom.: 21043 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.580

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.516 AC: 78410 AN: 151976 Hom.: 21046 Cov.: 33 AF XY: 0.519 AC XY: 38533 AN XY: 74284

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.580

Gnomad4 OTH AF: 0.491

Alfa AF: 0.538 Hom.: 3954

Bravo AF: 0.507

Asia WGS AF: 0.550 AC: 1914 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	0.12
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs261137; hg19: chr5-4361120;