Genetic Variant C12orf75:c.72-5298G>A (chr12-105360509-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.361

Publications

4 publications found

Variant links:

Genes affected

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

C12orf75 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C12orf75	NM_001145199.2 link	c.72-5298G>A		intron_variant	Intron 2 of 5	ENST00000443585.6	NP_001138671.1	Q8TAD7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf75	ENST00000443585.6 link	c.72-5298G>A		intron_variant	Intron 2 of 5	2	NM_001145199.2	ENSP00000448536.2		Q8TAD7

Frequencies

GnomAD3 genomes

AF:

0.468

AC:

71092

AN:

151902

Hom.:

17945

Cov.:

show subpopulations

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.:

AF XY:

0.471

AC XY:

35039

AN XY:

74320

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1850

3699

5549

7398

9248

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.027

(source)

DANN

Benign

0.65

PhyloP100

-0.36

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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12-105360509-G-A

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over