ENST00000549893.5:c.72-3928C>G

Variant names:

• chr12-105391704-C-G
• rs1368254
• ENST00000549893.5:c.72-3928C>G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

Genes affected

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

LOC105369957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369957	XR_001749297.2	n.3748+3515C>G		intron_variant	Intron 1 of 2
LOC105369957	XR_007063437.1	n.4419-3928C>G		intron_variant	Intron 1 of 3
LOC105369957	XR_945299.3	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	c.72-3928C>G		intron_variant	Intron 2 of 2	3		ENSP00000449096.1

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87694 AN: 151930 Hom.: 26003 Cov.: 32

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.: 32 AF XY: 0.586 AC XY: 43587 AN XY: 74330

Gnomad4 AFR AF: 0.686

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.617

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.586

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
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368254; hg19: chr12-105785482;