5-4343874-C-T

Variant names:

• chr5-4343874-C-T
• rs261159

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 0.528 in 151,968 control chromosomes in the GnomAD database, including 21,981 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 0.53 (21981 hom., cov: 32)
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.529 AC: 80271 AN: 151848 Hom.: 21979 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.586

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.528 AC: 80306 AN: 151968 Hom.: 21981 Cov.: 32 AF XY: 0.531 AC XY: 39453 AN XY: 74314

African (AFR) AF: 0.390 AC: 16155 AN: 41428

American (AMR) AF: 0.550 AC: 8409 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1867 AN: 3470

East Asian (EAS) AF: 0.678 AC: 3480 AN: 5136

South Asian (SAS) AF: 0.528 AC: 2539 AN: 4810

European-Finnish (FIN) AF: 0.600 AC: 6348 AN: 10574

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.586 AC: 39837 AN: 67944

Other (OTH) AF: 0.495 AC: 1046 AN: 2112

Alfa AF: 0.568 Hom.: 12488

Bravo AF: 0.520

Asia WGS AF: 0.571 AC: 1987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.53
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs261159; hg19: chr5-4343987;