12-42614099-C-T

Variant names:

• chr12-42614099-C-T
• rs12427230

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 0.072 in 152,004 control chromosomes in the GnomAD database, including 520 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 0.072 (520 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 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: 0.0720 AC: 10931 AN: 151886 Hom.: 518 Cov.: 31

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0615

Gnomad AMR AF: 0.0713

Gnomad ASJ AF: 0.0603

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0168

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0458

Gnomad OTH AF: 0.0886

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

GnomAD4 genome AF: 0.0720 AC: 10947 AN: 152004 Hom.: 520 Cov.: 31 AF XY: 0.0719 AC XY: 5341 AN XY: 74306

African (AFR) AF: 0.125 AC: 5167 AN: 41446

American (AMR) AF: 0.0712 AC: 1089 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0603 AC: 209 AN: 3464

East Asian (EAS) AF: 0.104 AC: 537 AN: 5160

South Asian (SAS) AF: 0.0168 AC: 81 AN: 4814

European-Finnish (FIN) AF: 0.0458 AC: 483 AN: 10546

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0458 AC: 3115 AN: 67970

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

Alfa AF: 0.0584 Hom.: 476

Bravo AF: 0.0785

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.45
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs12427230; hg19: chr12-43007901;