rs4964353

Positions:

• chr12-105282031-T-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C12orf75	ENST00000548458.6	n.68-44939T>C		intron_variant, non_coding_transcript_variant		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;