rs1504212

Variant names:

• chr5-53824125-C-A
• rs1504212

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 0.502 in 151,890 control chromosomes in the GnomAD database, including 19,630 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 0.50 (19630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.541 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: 0.502 AC: 76152 AN: 151772 Hom.: 19620 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.502 AC: 76203 AN: 151890 Hom.: 19630 Cov.: 32 AF XY: 0.495 AC XY: 36740 AN XY: 74204

African (AFR) AF: 0.473 AC: 19549 AN: 41370

American (AMR) AF: 0.483 AC: 7370 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1970 AN: 3466

East Asian (EAS) AF: 0.234 AC: 1213 AN: 5174

South Asian (SAS) AF: 0.314 AC: 1508 AN: 4810

European-Finnish (FIN) AF: 0.541 AC: 5698 AN: 10530

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

European-Non Finnish (NFE) AF: 0.546 AC: 37108 AN: 67974

Other (OTH) AF: 0.494 AC: 1043 AN: 2110

Alfa AF: 0.516 Hom.: 2849

Bravo AF: 0.500

Asia WGS AF: 0.296 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.019
DANN	Benign	0.15
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1504212; hg19: chr5-53119955;