rs10783969

Positions:

• chr12-39659356-T-G

Variant summary

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

The NM_001031748.4(C12orf40):​c.686+9002T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.793 in 151,824 control chromosomes in the GnomAD database, including 48,430 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 0.79 (48430 hom., cov: 31)
• Consequence: C12orf40 NM_001031748.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35

Genes affected

C12orf40 (HGNC:26846): (regulator of DNA class I crossover intermediates 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C12orf40	NM_001031748.4	c.686+9002T>G		intron_variant		ENST00000324616.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C12orf40	ENST00000324616.9	c.686+9002T>G		intron_variant		1	NM_001031748.4	P1
C12orf40	ENST00000405531.7	c.686+9002T>G		intron_variant		1
C12orf40	ENST00000468200.2	c.455+9002T>G		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.793 AC: 120264 AN: 151706 Hom.: 48407 Cov.: 31

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.793 AC: 120345 AN: 151824 Hom.: 48430 Cov.: 31 AF XY: 0.791 AC XY: 58686 AN XY: 74202

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.809

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.736

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.796

Alfa AF: 0.822 Hom.: 6665

Bravo AF: 0.784

Asia WGS AF: 0.671 AC: 2330 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.42

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10783969; hg19: chr12-40053158;