rs164561

Variant names:

• chr5-69044501-C-T
• rs164561

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 0.467 in 152,092 control chromosomes in the GnomAD database, including 16,758 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 0.47 (16758 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.515 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: 0.467 AC: 70973 AN: 151974 Hom.: 16740 Cov.: 33

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.444

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.467 AC: 71026 AN: 152092 Hom.: 16758 Cov.: 33 AF XY: 0.466 AC XY: 34655 AN XY: 74344

African (AFR) AF: 0.436 AC: 18077 AN: 41484

American (AMR) AF: 0.524 AC: 8011 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1764 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2602 AN: 5180

South Asian (SAS) AF: 0.400 AC: 1929 AN: 4824

European-Finnish (FIN) AF: 0.444 AC: 4697 AN: 10568

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32558 AN: 67978

Other (OTH) AF: 0.458 AC: 965 AN: 2108

Alfa AF: 0.473 Hom.: 16261

Bravo AF: 0.471

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.055
DANN	Benign	0.34
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs164561; hg19: chr5-68340328;