rs1504212

chr5-53824125-C-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;