rs1504212

Variant names:

• chr5-53824125-C-A
• rs1504212

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.494

Alfa AF: 0.518 Hom.: 2767

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504212; hg19: chr5-53119955;