rs294588

Variant names:

• chr5-163571509-T-C
• rs294588

Your query was ambiguous. Multiple possible variants found:

• chr5-163571509-T-C
• chr5-163571509-T-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.701 in 152,112 control chromosomes in the GnomAD database, including 37,807 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 0.70 (37807 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.886
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.701 AC: 106581 AN: 151994 Hom.: 37764 Cov.: 33

Gnomad AFR AF: 0.760

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.701 AC: 106679 AN: 152112 Hom.: 37807 Cov.: 33 AF XY: 0.698 AC XY: 51872 AN XY: 74346

African (AFR) AF: 0.760 AC: 31537 AN: 41498

American (AMR) AF: 0.751 AC: 11467 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2473 AN: 3470

East Asian (EAS) AF: 0.919 AC: 4761 AN: 5180

South Asian (SAS) AF: 0.676 AC: 3253 AN: 4810

European-Finnish (FIN) AF: 0.548 AC: 5788 AN: 10566

Middle Eastern (MID) AF: 0.648 AC: 188 AN: 290

European-Non Finnish (NFE) AF: 0.663 AC: 45080 AN: 68000

Other (OTH) AF: 0.733 AC: 1550 AN: 2116

Alfa AF: 0.692 Hom.: 53217

Bravo AF: 0.725

Asia WGS AF: 0.800 AC: 2783 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	17
DANN	Benign	0.80
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs294588; hg19: chr5-162998515; COSMIC: COSV56539576;