5-79541733-A-T

Variant names:

• chr5-79541733-A-T
• rs736201

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 0.546 in 152,248 control chromosomes in the GnomAD database, including 25,472 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 0.55 (25472 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 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: 0.546 AC: 83030 AN: 152130 Hom.: 25418 Cov.: 34

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.546 AC: 83146 AN: 152248 Hom.: 25472 Cov.: 34 AF XY: 0.549 AC XY: 40882 AN XY: 74444

African (AFR) AF: 0.827 AC: 34392 AN: 41566

American (AMR) AF: 0.558 AC: 8547 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1303 AN: 3472

East Asian (EAS) AF: 0.613 AC: 3179 AN: 5184

South Asian (SAS) AF: 0.357 AC: 1724 AN: 4826

European-Finnish (FIN) AF: 0.539 AC: 5701 AN: 10580

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26626 AN: 67996

Other (OTH) AF: 0.511 AC: 1080 AN: 2112

Alfa AF: 0.343 Hom.: 1026

Bravo AF: 0.567

Asia WGS AF: 0.523 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs736201; hg19: chr5-78837556; COSMIC: COSV50461280;