12-103239351-C-T

Variant names:

• chr12-103239351-C-T
• rs10507159
• NM_001386867.1:c.320+37799G>A

Variant summary

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

The NM_001386867.1(C12orf42):​c.320+37799G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 152,166 control chromosomes in the GnomAD database, including 495 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 0.052 (495 hom., cov: 32)
• Consequence: C12orf42 NM_001386867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf42	NM_001386867.1	c.320+37799G>A		intron_variant	Intron 5 of 6		NP_001373796.1
C12orf42	NR_103526.2	n.1779-1449G>A		intron_variant	Intron 10 of 10
C12orf42	NR_170332.1	n.1582+23975G>A		intron_variant	Intron 8 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf42	ENST00000547347.5	n.*1367-1449G>A		intron_variant	Intron 10 of 10	2		ENSP00000446908.1

Frequencies

GnomAD3 genomes AF: 0.0517 AC: 7865 AN: 152048 Hom.: 497 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0306

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00773

Gnomad OTH AF: 0.0465

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

GnomAD4 genome AF: 0.0517 AC: 7871 AN: 152166 Hom.: 495 Cov.: 32 AF XY: 0.0509 AC XY: 3788 AN XY: 74402

African (AFR) AF: 0.154 AC: 6406 AN: 41502

American (AMR) AF: 0.0251 AC: 384 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3470

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0150 AC: 72 AN: 4814

European-Finnish (FIN) AF: 0.0306 AC: 324 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.00774 AC: 526 AN: 68002

Other (OTH) AF: 0.0460 AC: 97 AN: 2110

Alfa AF: 0.0241 Hom.: 53

Bravo AF: 0.0567

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.37
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs10507159; hg19: chr12-103633129;