rs1504464

Variant names:

• chr12-60349398-C-T
• rs1504464

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 0.424 in 151,816 control chromosomes in the GnomAD database, including 15,578 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 0.42 (15578 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.558 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: 0.424 AC: 64333 AN: 151700 Hom.: 15568 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.569

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.424 AC: 64353 AN: 151816 Hom.: 15578 Cov.: 31 AF XY: 0.425 AC XY: 31521 AN XY: 74170

African (AFR) AF: 0.177 AC: 7344 AN: 41450

American (AMR) AF: 0.568 AC: 8667 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1862 AN: 3466

East Asian (EAS) AF: 0.568 AC: 2901 AN: 5106

South Asian (SAS) AF: 0.457 AC: 2200 AN: 4812

European-Finnish (FIN) AF: 0.446 AC: 4693 AN: 10512

Middle Eastern (MID) AF: 0.462 AC: 134 AN: 290

European-Non Finnish (NFE) AF: 0.516 AC: 35070 AN: 67918

Other (OTH) AF: 0.470 AC: 989 AN: 2106

Alfa AF: 0.458 Hom.: 2267

Bravo AF: 0.424

Asia WGS AF: 0.553 AC: 1922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.19
DANN	Benign	0.94
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs1504464; hg19: chr12-60743179;