rs26595

chr5-116423793-G-Achr5-116423793-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 0.441 in 152,024 control chromosomes in the GnomAD database, including 17,697 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 0.44 (17697 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253

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 (NFE) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67021 AN: 151904 Hom.: 17701 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.757

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.441 AC: 67007 AN: 152024 Hom.: 17697 Cov.: 32 AF XY: 0.439 AC XY: 32641 AN XY: 74304

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.586

Gnomad4 OTH AF: 0.446

Alfa AF: 0.549 Hom.: 34077

Bravo AF: 0.412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.69
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs26595; hg19: chr5-115759490;