Genetic Variant NM_001322331.2:c.-13+2026A>G (chr2-119364764-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

14 publications found

Variant links:

Genes affected

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

C2orf76 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C2orf76	NM_001322331.2 link	c.-13+2026A>G		intron_variant	Intron 1 of 5	ENST00000334816.12	NP_001309260.1	Q3KRA6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C2orf76	ENST00000334816.12 link	c.-13+2026A>G		intron_variant	Intron 1 of 5	1	NM_001322331.2	ENSP00000335041.7		Q3KRA6

Frequencies

GnomAD3 genomes

AF:

0.290

AC:

44035

AN:

151820

Hom.:

6550

Cov.:

show subpopulations

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.:

AF XY:

0.289

AC XY:

21438

AN XY:

74262

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.293

AC:

19883

AN:

67952

Other (OTH)

AF:

0.254

AC:

536

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1594

3187

4781

6374

7968

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.0

(source)

DANN

Benign

0.69

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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NM_001322331.2:c.-13+2026A>G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over