5-26139029-A-T

Position:

• chr5-26139029-A-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 0.0836 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0730

Gnomad4 ASJ AF: 0.0743

Gnomad4 EAS AF: 0.0725

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0553

Gnomad4 NFE AF: 0.0628

Gnomad4 OTH AF: 0.0900

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4701523; hg19: chr5-26139138;