rs10861406

chr12-105360509-G-Achr12-105360509-G-Cchr12-105360509-G-T

Variant summary

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

The NM_001145199.2(C12orf75):c.72-5298G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,020 control chromosomes in the GnomAD database, including 17,990 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 0.47 (17990 hom., cov: 32)
• Consequence: C12orf75 NM_001145199.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.361

Genes affected

C12orf75 (HGNC:35164): (chromosome 12 open reading frame 75)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C12orf75	NM_001145199.2	c.72-5298G>A		intron_variant		ENST00000443585.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C12orf75	ENST00000443585.6	c.72-5298G>A		intron_variant		2	NM_001145199.2	P1

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71092 AN: 151902 Hom.: 17945 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.468 AC: 71199 AN: 152020 Hom.: 17990 Cov.: 32 AF XY: 0.471 AC XY: 35039 AN XY: 74320

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.484

Alfa AF: 0.401 Hom.: 6444

Bravo AF: 0.487

Asia WGS AF: 0.616 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.027
Dann	Benign	0.65

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: rs10861406; hg19: chr12-105754287;