Genetic Variant C12orf75:c.72-3928C>G (chr12-105391704-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000549893.5(C12orf75):c.72-3928C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,048 control chromosomes in the GnomAD database, including 26,039 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 0.58 ( 26039 hom., cov: 32)

Consequence

C12orf75
ENST00000549893.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0220

Publications

4 publications found

Variant links:

Genes affected

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

C12orf75 links:

LOC105369957 (HGNC:):

LOC105369957 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105369957	XR_001749297.2 link	n.3748+3515C>G	intron_variant	Intron 1 of 2
LOC105369957	XR_007063437.1 link	n.4419-3928C>G	intron_variant	Intron 1 of 3
LOC105369957	XR_945299.3 link	n.748+3515C>G	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf75	ENST00000549893.5 link	c.72-3928C>G		intron_variant	Intron 2 of 2	3		ENSP00000449096.1		F8VXK5

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87694

AN:

151930

Hom.:

26003

Cov.:

show subpopulations

Gnomad AFR

AF:

0.686

Gnomad AMI

AF:

0.563

Gnomad AMR

AF:

0.585

Gnomad ASJ

AF:

0.505

Gnomad EAS

AF:

0.721

Gnomad SAS

AF:

0.677

Gnomad FIN

AF:

0.617

Gnomad MID

AF:

0.554

Gnomad NFE

AF:

0.489

Gnomad OTH

AF:

0.584

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

GnomAD4 genome

AF:

0.577

AC:

87784

AN:

152048

Hom.:

26039

Cov.:

AF XY:

0.586

AC XY:

43587

AN XY:

74330

show subpopulations

African (AFR)

AF:

0.686

AC:

28446

AN:

41464

American (AMR)

AF:

0.585

AC:

8943

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.505

AC:

1751

AN:

3470

East Asian (EAS)

AF:

0.721

AC:

3724

AN:

5168

South Asian (SAS)

AF:

0.676

AC:

3263

AN:

4824

European-Finnish (FIN)

AF:

0.617

AC:

6520

AN:

10566

Middle Eastern (MID)

AF:

0.554

AC:

163

AN:

294

European-Non Finnish (NFE)

AF:

0.489

AC:

33230

AN:

67970

Other (OTH)

AF:

0.586

AC:

1233

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1873

3746

5619

7492

9365

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.401

Hom.:

1058

Bravo

AF:

0.577

Asia WGS

AF:

0.701

AC:

2439

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.3

(source)

DANN

Benign

0.34

PhyloP100

0.022

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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chr12-105391704-C-G

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