12-105360509-G-A

Variant names:

• chr12-105360509-G-A
• rs10861406
• NM_001145199.2:c.72-5298G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145199.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf75	NM_001145199.2	MANE Select	c.72-5298G>A		intron	N/A	NP_001138671.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf75	ENST00000443585.6	TSL:2 MANE Select	c.72-5298G>A		intron	N/A	ENSP00000448536.2
	C12orf75	ENST00000612117.4	TSL:1	c.72-6108G>A		intron	N/A	ENSP00000479631.1
	C12orf75	ENST00000549934.2	TSL:3	c.72-5298G>A		intron	N/A	ENSP00000450095.2

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

African (AFR) AF: 0.638 AC: 26443 AN: 41436

American (AMR) AF: 0.505 AC: 7714 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3468

East Asian (EAS) AF: 0.677 AC: 3511 AN: 5184

South Asian (SAS) AF: 0.535 AC: 2574 AN: 4812

European-Finnish (FIN) AF: 0.332 AC: 3502 AN: 10562

Middle Eastern (MID) AF: 0.424 AC: 123 AN: 290

European-Non Finnish (NFE) AF: 0.359 AC: 24428 AN: 67958

Other (OTH) AF: 0.484 AC: 1021 AN: 2110

Alfa AF: 0.401 Hom.: 7179

Bravo AF: 0.487

Asia WGS AF: 0.616 AC: 2146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.027
DANN	Benign	0.65
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10861406; hg19: chr12-105754287;