rs2098435

chr12-14851655-G-A

Variant summary

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

The ENST00000527783.1(C12orf60):n.76-47514G>A 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 0.44 in 151,968 control chromosomes in the GnomAD database, including 15,198 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 0.44 (15198 hom., cov: 32)
• Consequence: C12orf60 ENST00000527783.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

Genes affected

C12orf60 (HGNC:28726): (chromosome 12 open reading frame 60)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 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
C12orf60	ENST00000527783.1	n.76-47514G>A		intron_variant, non_coding_transcript_variant		2
C12orf60	ENST00000533472.1	n.86+47904G>A		intron_variant, non_coding_transcript_variant		3
C12orf60	ENST00000648334.1	n.125+21976G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66813 AN: 151848 Hom.: 15169 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.440 AC: 66886 AN: 151968 Hom.: 15198 Cov.: 32 AF XY: 0.436 AC XY: 32421 AN XY: 74296

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.431

Alfa AF: 0.446 Hom.: 13792

Bravo AF: 0.440

Asia WGS AF: 0.304 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.17
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2098435; hg19: chr12-15004589;