chr12-60349398-C-T

Variant names:

• chr12-60349398-C-T
• rs1504464

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 0.424 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.470

Alfa AF: 0.469 Hom.: 2252

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1504464; hg19: chr12-60743179;