12-61070001-T-C

Position:

• chr12-61070001-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.359 in 151,778 control chromosomes in the GnomAD database, including 10,928 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 0.36 (10928 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 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: 0.359 AC: 54500 AN: 151660 Hom.: 10911 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.359 AC: 54522 AN: 151778 Hom.: 10928 Cov.: 32 AF XY: 0.367 AC XY: 27243 AN XY: 74182

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.511

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.375

Alfa AF: 0.400 Hom.: 2262

Bravo AF: 0.361

Asia WGS AF: 0.421 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	18
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11173732; hg19: chr12-61463782;