Variant rs1919127 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032266.5(C2orf16):c.12266T>C(p.Val4089Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 1,613,376 control chromosomes in the GnomAD database, including 65,269 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 6335 hom., cov: 32)

Exomes 𝑓: 0.27 ( 58934 hom. )

Consequence

C2orf16
NM_032266.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.392

Variant links:

Genes affected

C2orf16 (HGNC:25275): (SPATA31 subfamily H member 1) Located in extracellular exosome and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

C2orf16 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.4241209E-4).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2orf16	NM_032266.5 linkuse as main transcript	c.12266T>C	p.Val4089Ala	missense_variant	5/5	ENST00000447166.3	NP_115642.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2orf16	ENST00000447166.3 linkuse as main transcript	c.12266T>C	p.Val4089Ala	missense_variant	5/5	3	NM_032266.5	ENSP00000403181	P1

Frequencies

GnomAD3 genomes

AF:

0.276

AC:

41961

AN:

151966

Hom.:

6332

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.192

Gnomad AMR

AF:

0.450

Gnomad ASJ

AF:

0.339

Gnomad EAS

AF:

0.488

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.341

Gnomad NFE

AF:

0.271

Gnomad OTH

AF:

0.325

GnomAD3 exomes

AF:

0.312

AC:

77801

AN:

248980

Hom.:

13895

AF XY:

0.299

AC XY:

40423

AN XY:

135084

show subpopulations

Gnomad AFR exome

AF:

0.187

Gnomad AMR exome

AF:

0.528

Gnomad ASJ exome

AF:

0.338

Gnomad EAS exome

AF:

0.478

Gnomad SAS exome

AF:

0.197

Gnomad FIN exome

AF:

0.289

Gnomad NFE exome

AF:

0.271

Gnomad OTH exome

AF:

0.311

GnomAD4 exome

AF:

0.274

AC:

400940

AN:

1461292

Hom.:

58934

Cov.:

AF XY:

0.272

AC XY:

197757

AN XY:

726962

show subpopulations

Gnomad4 AFR exome

AF:

0.181

Gnomad4 AMR exome

AF:

0.514

Gnomad4 ASJ exome

AF:

0.338

Gnomad4 EAS exome

AF:

0.535

Gnomad4 SAS exome

AF:

0.200

Gnomad4 FIN exome

AF:

0.285

Gnomad4 NFE exome

AF:

0.261

Gnomad4 OTH exome

AF:

0.284

GnomAD4 genome

AF:

0.276

AC:

41972

AN:

152084

Hom.:

6335

Cov.:

AF XY:

0.281

AC XY:

20918

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.191

Gnomad4 AMR

AF:

0.451

Gnomad4 ASJ

AF:

0.339

Gnomad4 EAS

AF:

0.489

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.272

Gnomad4 OTH

AF:

0.325

Alfa

AF:

0.279

Hom.:

10660

Bravo

AF:

0.289

TwinsUK

AF:

0.255

AC:

947

ALSPAC

AF:

0.255

AC:

982

ESP6500AA

AF:

0.184

AC:

687

ESP6500EA

AF:

0.270

AC:

2218

ExAC

AF:

0.297

AC:

35861

Asia WGS

AF:

0.303

AC:

1056

AN:

3478

EpiCase

AF:

0.294

EpiControl

AF:

0.292

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.75

BayesDel_noAF

Benign

-0.71

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.0025

.;T

Eigen

Benign

-0.73

Eigen_PC

Benign

-0.75

FATHMM_MKL

Benign

0.024

LIST_S2

Benign

0.42

T;T

MetaRNN

Benign

0.00024

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.55

.;N

MutationTaster

Benign

1.0

PROVEAN

Benign

-1.1

.;N

REVEL

Benign

0.027

Sift

Benign

0.30

.;T

Sift4G

Benign

0.43

.;T

Polyphen

0.41

.;B

Vest4

0.023

MPC

0.14

ClinPred

0.0039

GERP RS

1.8

Varity_R

0.045

gMVP

0.045

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over