rs12613135

Variant names:

• chr2-119364764-T-C
• rs12613135
• NM_001322331.2:c.-13+2026A>G

Variant summary

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

The NM_001322331.2(C2orf76):​c.-13+2026A>G 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 151,940 control chromosomes in the GnomAD database, including 6,562 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 (6562 hom., cov: 32)
• Consequence: C2orf76 NM_001322331.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 14 publications found

Genes affected

C2orf76 (HGNC:27017): (chromosome 2 open reading frame 76)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001322331.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf76	NM_001322331.2	MANE Select	c.-13+2026A>G		intron	N/A	NP_001309260.1	Q3KRA6
	C2orf76	NM_001017927.4		c.-216+1593A>G		intron	N/A	NP_001017927.2	Q3KRA6
	C2orf76	NM_001322329.2		c.-216+1672A>G		intron	N/A	NP_001309258.1	Q3KRA6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf76	ENST00000334816.12	TSL:1 MANE Select	c.-13+2026A>G		intron	N/A	ENSP00000335041.7	Q3KRA6
	C2orf76	ENST00000409466.6	TSL:1	c.-216+1672A>G		intron	N/A	ENSP00000386302.2	Q3KRA6
	C2orf76	ENST00000409523.1	TSL:1	c.-13+1593A>G		intron	N/A	ENSP00000386714.1	Q3KRA6

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44035 AN: 151820 Hom.: 6550 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.290 AC: 44082 AN: 151940 Hom.: 6562 Cov.: 32 AF XY: 0.289 AC XY: 21438 AN XY: 74262

African (AFR) AF: 0.331 AC: 13697 AN: 41412

American (AMR) AF: 0.226 AC: 3452 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1630 AN: 5170

South Asian (SAS) AF: 0.299 AC: 1438 AN: 4812

European-Finnish (FIN) AF: 0.235 AC: 2474 AN: 10550

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19883 AN: 67952

Other (OTH) AF: 0.254 AC: 536 AN: 2108

Alfa AF: 0.286 Hom.: 10520

Bravo AF: 0.289

Asia WGS AF: 0.301 AC: 1045 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12613135; hg19: chr2-120122340;