Variant 16-4556604-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001145011.2(C16orf96):c.115A>G(p.Met39Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00751 in 1,551,674 control chromosomes in the GnomAD database, including 69 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0046 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0078 ( 65 hom. )

Consequence

C16orf96
NM_001145011.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0850

Variant links:

Genes affected

C16orf96 (HGNC:40031): (chromosome 16 open reading frame 96)

C16orf96 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0045820475).

BP6

Variant 16-4556604-A-G is Benign according to our data. Variant chr16-4556604-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2646150.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C16orf96	NM_001145011.2 link	c.115A>G	p.Met39Val	missense_variant	1/16	ENST00000444310.5	NP_001138483.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C16orf96	ENST00000444310.5 link	c.115A>G	p.Met39Val	missense_variant	1/16	5	NM_001145011.2	ENSP00000415027.3		A6NNT2

Frequencies

GnomAD3 genomes

AF:

0.00457

AC:

696

AN:

152150

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00169

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00347

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00292

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00766

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00420

AC:

657

AN:

156426

Hom.:

AF XY:

0.00422

AC XY:

350

AN XY:

82922

show subpopulations

Gnomad AFR exome

AF:

0.00177

Gnomad AMR exome

AF:

0.00243

Gnomad ASJ exome

AF:

0.00354

Gnomad EAS exome

AF:

0.0000918

Gnomad SAS exome

AF:

0.000615

Gnomad FIN exome

AF:

0.00250

Gnomad NFE exome

AF:

0.00784

Gnomad OTH exome

AF:

0.00500

GnomAD4 exome

AF:

0.00783

AC:

10952

AN:

1399406

Hom.:

Cov.:

AF XY:

0.00762

AC XY:

5260

AN XY:

690206

show subpopulations

Gnomad4 AFR exome

AF:

0.00139

Gnomad4 AMR exome

AF:

0.00272

Gnomad4 ASJ exome

AF:

0.00357

Gnomad4 EAS exome

AF:

0.0000560

Gnomad4 SAS exome

AF:

0.000568

Gnomad4 FIN exome

AF:

0.00418

Gnomad4 NFE exome

AF:

0.00931

Gnomad4 OTH exome

AF:

0.00717

GnomAD4 genome

AF:

0.00456

AC:

695

AN:

152268

Hom.:

Cov.:

AF XY:

0.00423

AC XY:

315

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.00347

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00292

Gnomad4 NFE

AF:

0.00766

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00732

Hom.:

Bravo

AF:

0.00473

TwinsUK

AF:

0.00647

AC:

ALSPAC

AF:

0.00856

AC:

ESP6500AA

AF:

0.000723

AC:

ESP6500EA

AF:

0.00880

AC:

ExAC

AF:

0.00294

AC:

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

C16orf96: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.44

CADD

Benign

9.0

DANN

Benign

0.64

DEOGEN2

Benign

0.0062

Eigen

Benign

-0.76

Eigen_PC

Benign

-0.96

FATHMM_MKL

Benign

0.053

LIST_S2

Benign

0.56

M_CAP

Benign

0.011

MetaRNN

Benign

0.0046

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.55

PROVEAN

Benign

-1.2

REVEL

Benign

0.060

Sift

Uncertain

0.020

Sift4G

Uncertain

0.047

Polyphen

0.60

Vest4

0.36

MVP

0.099

ClinPred

0.039

GERP RS

-5.4

Varity_R

0.18

gMVP

0.15

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over