5-25944837-T-C

Variant names:

• chr5-25944837-T-C
• rs6894838

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 0.633 in 151,678 control chromosomes in the GnomAD database, including 30,794 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 0.63 (30794 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.633 AC: 95989 AN: 151560 Hom.: 30758 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.633 AC: 96084 AN: 151678 Hom.: 30794 Cov.: 32 AF XY: 0.634 AC XY: 46998 AN XY: 74140

African (AFR) AF: 0.672 AC: 27846 AN: 41428

American (AMR) AF: 0.687 AC: 10445 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3466

East Asian (EAS) AF: 0.845 AC: 4306 AN: 5094

South Asian (SAS) AF: 0.683 AC: 3297 AN: 4824

European-Finnish (FIN) AF: 0.547 AC: 5771 AN: 10556

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40597 AN: 67802

Other (OTH) AF: 0.630 AC: 1327 AN: 2108

Alfa AF: 0.615 Hom.: 15498

Bravo AF: 0.645

Asia WGS AF: 0.734 AC: 2551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.70
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs6894838; hg19: chr5-25944946;