rs2098435

Variant names:

• chr12-14851655-G-A
• rs2098435
• ENST00000527783.1:n.76-47514G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527783.1(C12orf60):​n.76-47514G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 10 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C12orf60	ENST00000527783.1	n.76-47514G>A		intron_variant	Intron 1 of 3	2
C12orf60	ENST00000533472.1	n.86+47904G>A		intron_variant	Intron 1 of 1	3
C12orf60	ENST00000648334.1	n.125+21976G>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.479 AC: 19829 AN: 41426

American (AMR) AF: 0.421 AC: 6430 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1341 AN: 3468

East Asian (EAS) AF: 0.121 AC: 626 AN: 5182

South Asian (SAS) AF: 0.450 AC: 2170 AN: 4824

European-Finnish (FIN) AF: 0.401 AC: 4217 AN: 10526

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30756 AN: 67964

Other (OTH) AF: 0.431 AC: 906 AN: 2104

Alfa AF: 0.448 Hom.: 18558

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
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2098435; hg19: chr12-15004589;