12-61155300-C-T

Variant names:

• chr12-61155300-C-T
• rs17124610

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 0.0327 in 151,926 control chromosomes in the GnomAD database, including 128 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 0.033 (128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.138 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: 0.0327 AC: 4961 AN: 151808 Hom.: 129 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0205

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0733

Gnomad FIN AF: 0.0181

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0287

Gnomad OTH AF: 0.0341

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

GnomAD4 genome AF: 0.0327 AC: 4962 AN: 151926 Hom.: 128 Cov.: 32 AF XY: 0.0334 AC XY: 2477 AN XY: 74248

African (AFR) AF: 0.0304 AC: 1260 AN: 41478

American (AMR) AF: 0.0204 AC: 311 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3466

East Asian (EAS) AF: 0.147 AC: 754 AN: 5144

South Asian (SAS) AF: 0.0725 AC: 350 AN: 4828

European-Finnish (FIN) AF: 0.0181 AC: 192 AN: 10602

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0287 AC: 1949 AN: 67890

Other (OTH) AF: 0.0333 AC: 70 AN: 2102

Alfa AF: 0.0269 Hom.: 65

Bravo AF: 0.0318

Asia WGS AF: 0.100 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs17124610; hg19: chr12-61549081;