XM_047428802.1:c.36+6847A>G

Variant names:

• chr12-103517265-T-C
• rs17034045
• XM_047428802.1:c.36+6847A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047428802.1(C12orf42):​c.36+6847A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0995 in 152,254 control chromosomes in the GnomAD database, including 985 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 0.10 (985 hom., cov: 32)
• Consequence: C12orf42 XM_047428802.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 3 publications found

Genes affected

C12orf42 (HGNC:24729): (chromosome 12 open reading frame 42)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0994 AC: 15129 AN: 152136 Hom.: 981 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0688

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.0495

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0995 AC: 15156 AN: 152254 Hom.: 985 Cov.: 32 AF XY: 0.102 AC XY: 7611 AN XY: 74448

African (AFR) AF: 0.129 AC: 5370 AN: 41536

American (AMR) AF: 0.0687 AC: 1051 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1353 AN: 5184

South Asian (SAS) AF: 0.268 AC: 1293 AN: 4824

European-Finnish (FIN) AF: 0.0495 AC: 525 AN: 10612

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0714 AC: 4858 AN: 68006

Other (OTH) AF: 0.104 AC: 219 AN: 2114

Alfa AF: 0.0820 Hom.: 97

Bravo AF: 0.0991

Asia WGS AF: 0.276 AC: 958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.45
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs17034045; hg19: chr12-103911043; COSMIC: COSV50457705;