5-26139029-A-T

Variant names:

• chr5-26139029-A-T
• rs4701523

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 0.0836 in 152,206 control chromosomes in the GnomAD database, including 613 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 0.084 (613 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 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: 0.0836 AC: 12718 AN: 152088 Hom.: 611 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0731

Gnomad ASJ AF: 0.0743

Gnomad EAS AF: 0.0726

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0836 AC: 12724 AN: 152206 Hom.: 613 Cov.: 32 AF XY: 0.0834 AC XY: 6209 AN XY: 74430

African (AFR) AF: 0.127 AC: 5268 AN: 41510

American (AMR) AF: 0.0730 AC: 1114 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0743 AC: 258 AN: 3472

East Asian (EAS) AF: 0.0725 AC: 376 AN: 5184

South Asian (SAS) AF: 0.122 AC: 590 AN: 4826

European-Finnish (FIN) AF: 0.0553 AC: 587 AN: 10620

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0628 AC: 4272 AN: 68008

Other (OTH) AF: 0.0900 AC: 190 AN: 2110

Alfa AF: 0.0574 Hom.: 133

Bravo AF: 0.0858

Asia WGS AF: 0.124 AC: 433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs4701523; hg19: chr5-26139138;