rs11693629

Variant names:

• chr2-119365701-C-T
• rs11693629
• NM_001322331.2:c.-13+1089G>A

Variant summary

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

The NM_001017927.4(C2orf76):​c.-216+656G>A 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 152,016 control chromosomes in the GnomAD database, including 6,569 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 (6569 hom., cov: 32)
• Consequence: C2orf76 NM_001017927.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.299
• Publications: 8 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=-0.9).
• 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_001017927.4. 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+1089G>A		intron	N/A	NP_001309260.1
	C2orf76	NM_001017927.4		c.-216+656G>A		intron	N/A	NP_001017927.2
	C2orf76	NM_001322329.2		c.-216+735G>A		intron	N/A	NP_001309258.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C2orf76	ENST00000334816.12	TSL:1 MANE Select	c.-13+1089G>A		intron	N/A	ENSP00000335041.7
	C2orf76	ENST00000409466.6	TSL:1	c.-216+735G>A		intron	N/A	ENSP00000386302.2
	C2orf76	ENST00000409523.1	TSL:1	c.-13+656G>A		intron	N/A	ENSP00000386714.1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44063 AN: 151898 Hom.: 6557 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: 0.247

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

GnomAD4 genome AF: 0.290 AC: 44110 AN: 152016 Hom.: 6569 Cov.: 32 AF XY: 0.289 AC XY: 21453 AN XY: 74296

African (AFR) AF: 0.331 AC: 13707 AN: 41440

American (AMR) AF: 0.226 AC: 3454 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 670 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1629 AN: 5170

South Asian (SAS) AF: 0.299 AC: 1439 AN: 4818

European-Finnish (FIN) AF: 0.235 AC: 2480 AN: 10546

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

European-Non Finnish (NFE) AF: 0.293 AC: 19894 AN: 67980

Other (OTH) AF: 0.254 AC: 535 AN: 2110

Alfa AF: 0.288 Hom.: 17608

Bravo AF: 0.289

Asia WGS AF: 0.303 AC: 1050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.53
PhyloP100		-0.30
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: rs11693629; hg19: chr2-120123277; COSMIC: COSV58346017; COSMIC: COSV58346017;