12-61070001-T-C

Variant names:

• chr12-61070001-T-C
• rs11173732

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.185 AC: 7676 AN: 41460

American (AMR) AF: 0.528 AC: 8022 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1448 AN: 3456

East Asian (EAS) AF: 0.511 AC: 2636 AN: 5158

South Asian (SAS) AF: 0.439 AC: 2119 AN: 4822

European-Finnish (FIN) AF: 0.456 AC: 4808 AN: 10544

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26592 AN: 67836

Other (OTH) AF: 0.375 AC: 790 AN: 2104

Alfa AF: 0.393 Hom.: 2275

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
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs11173732; hg19: chr12-61463782;