ENST00000548458.6:n.68-44939T>C

Variant names:

• chr12-105282031-T-C
• rs4964353
• ENST00000548458.6:n.68-44939T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000548458.6(C12orf75):​n.68-44939T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,144 control chromosomes in the GnomAD database, including 6,502 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 0.29 (6502 hom., cov: 32)
• Consequence: C12orf75 ENST00000548458.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.34

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf75	ENST00000548458.6	n.68-44939T>C		intron_variant	Intron 1 of 6	3

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44104 AN: 152026 Hom.: 6498 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.290 AC: 44119 AN: 152144 Hom.: 6502 Cov.: 32 AF XY: 0.291 AC XY: 21665 AN XY: 74388

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.278

Alfa AF: 0.300 Hom.: 1045

Bravo AF: 0.289

Asia WGS AF: 0.270 AC: 939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	18
DANN	Benign	0.96

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4964353; hg19: chr12-105675809;