5-165940226-A-T

Variant names:

• chr5-165940226-A-T
• rs17066124

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 0.391 in 152,044 control chromosomes in the GnomAD database, including 11,895 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 0.39 (11895 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.433 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: 0.391 AC: 59364 AN: 151924 Hom.: 11890 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.391 AC: 59386 AN: 152044 Hom.: 11895 Cov.: 32 AF XY: 0.391 AC XY: 29022 AN XY: 74312

African (AFR) AF: 0.438 AC: 18176 AN: 41466

American (AMR) AF: 0.293 AC: 4474 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1583 AN: 3472

East Asian (EAS) AF: 0.386 AC: 1995 AN: 5164

South Asian (SAS) AF: 0.365 AC: 1762 AN: 4822

European-Finnish (FIN) AF: 0.444 AC: 4690 AN: 10560

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25477 AN: 67964

Other (OTH) AF: 0.374 AC: 792 AN: 2116

Alfa AF: 0.381 Hom.: 1454

Bravo AF: 0.380

Asia WGS AF: 0.367 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.6
DANN	Benign	0.80
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs17066124; hg19: chr5-165367231;