rs261137

Variant names:

• chr5-4361007-C-T
• rs261137

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.370 AC: 15334 AN: 41450

American (AMR) AF: 0.542 AC: 8265 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1727 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3479 AN: 5160

South Asian (SAS) AF: 0.491 AC: 2363 AN: 4816

European-Finnish (FIN) AF: 0.598 AC: 6319 AN: 10570

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.580 AC: 39390 AN: 67936

Other (OTH) AF: 0.491 AC: 1038 AN: 2114

Alfa AF: 0.533 Hom.: 4009

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs261137; hg19: chr5-4361120;