rs10507169

Variant names:

• chr12-103533084-G-A
• rs10507169
• XM_047428803.1:c.-22+30563C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-103533084-G-A
• chr12-103533084-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047428803.1(C12orf42):​c.-22+30563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,084 control chromosomes in the GnomAD database, including 2,516 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 0.17 (2516 hom., cov: 32)
• Consequence: C12orf42 XM_047428803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

Genes affected

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

ENSG00000286197 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf42	XM_047428803.1	c.-22+30563C>T		intron_variant	Intron 1 of 5		XP_047284759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286197	ENST00000650784.1	n.205-13863C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25166 AN: 151966 Hom.: 2513 Cov.: 32

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.166 AC: 25177 AN: 152084 Hom.: 2516 Cov.: 32 AF XY: 0.171 AC XY: 12740 AN XY: 74340

Gnomad4 AFR AF: 0.0632

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.179

Alfa AF: 0.190 Hom.: 1421

Bravo AF: 0.148

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	15
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507169; hg19: chr12-103926862;