rs152543

Variant names:

• chr5-50946210-T-A
• rs152543

Your query was ambiguous. Multiple possible variants found:

• chr5-50946210-T-A
• chr5-50946210-T-C
• chr5-50946210-T-G

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 0.387 in 152,068 control chromosomes in the GnomAD database, including 12,307 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 (12307 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.826 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: 0.386 AC: 58724 AN: 151950 Hom.: 12289 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.387 AC: 58775 AN: 152068 Hom.: 12307 Cov.: 32 AF XY: 0.395 AC XY: 29339 AN XY: 74340

African (AFR) AF: 0.301 AC: 12487 AN: 41470

American (AMR) AF: 0.470 AC: 7184 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3470

East Asian (EAS) AF: 0.847 AC: 4389 AN: 5184

South Asian (SAS) AF: 0.595 AC: 2864 AN: 4812

European-Finnish (FIN) AF: 0.379 AC: 4007 AN: 10568

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 24985 AN: 67960

Other (OTH) AF: 0.398 AC: 839 AN: 2108

Alfa AF: 0.385 Hom.: 1463

Bravo AF: 0.388

Asia WGS AF: 0.697 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	5.0
DANN	Benign	0.88
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs152543; hg19: chr5-50242044; COSMIC: COSV60125150;