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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650784.1(ENSG00000286197):​n.205-13863C>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: ENSG00000286197 ENST00000650784.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74
• Publications: 2 publications found

Genes affected

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

ENSG00000286197 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650784.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286197	ENST00000650784.1		n.205-13863C>T		intron	N/A

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

African (AFR) AF: 0.0632 AC: 2622 AN: 41488

American (AMR) AF: 0.147 AC: 2248 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3468

East Asian (EAS) AF: 0.208 AC: 1075 AN: 5178

South Asian (SAS) AF: 0.321 AC: 1544 AN: 4812

European-Finnish (FIN) AF: 0.302 AC: 3190 AN: 10556

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13353 AN: 67972

Other (OTH) AF: 0.179 AC: 377 AN: 2112

Alfa AF: 0.188 Hom.: 1577

Bravo AF: 0.148

Asia WGS AF: 0.254 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	15
DANN	Benign	0.72
PhyloP100		1.7

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10507169;

hg19: chr12-103926862;