12-60349398-C-T

Position:

• chr12-60349398-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;