Variant 16-4575930-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001145011.2(C16orf96):c.1450C>T(p.Arg484Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00353 in 1,536,462 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0074 ( 6 hom., cov: 33)

Exomes 𝑓: 0.0031 ( 36 hom. )

Consequence

C16orf96
NM_001145011.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.82

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.005681157).

BP6

Variant 16-4575930-C-T is Benign according to our data. Variant chr16-4575930-C-T is described in ClinVar as [Benign]. Clinvar id is 771013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00311 (4300/1384236) while in subpopulation MID AF= 0.0219 (122/5580). AF 95% confidence interval is 0.0187. There are 36 homozygotes in gnomad4_exome. There are 2217 alleles in male gnomad4_exome subpopulation. Median coverage is 36. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C16orf96	NM_001145011.2 link	c.1450C>T	p.Arg484Cys	missense_variant	5/16	ENST00000444310.5	NP_001138483.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C16orf96	ENST00000444310.5 link	c.1450C>T	p.Arg484Cys	missense_variant	5/16	5	NM_001145011.2	ENSP00000415027.3		A6NNT2

Frequencies

GnomAD3 genomes

AF:

0.00738

AC:

1122

AN:

152108

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00179

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0117

Gnomad ASJ

AF:

0.0159

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0127

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00916

Gnomad OTH

AF:

0.0172

GnomAD3 exomes

AF:

0.00361

AC:

552

AN:

152864

Hom.:

AF XY:

0.00334

AC XY:

271

AN XY:

81082

show subpopulations

Gnomad AFR exome

AF:

0.00114

Gnomad AMR exome

AF:

0.00236

Gnomad ASJ exome

AF:

0.00424

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000396

Gnomad FIN exome

AF:

0.00859

Gnomad NFE exome

AF:

0.00501

Gnomad OTH exome

AF:

0.00351

GnomAD4 exome

AF:

0.00311

AC:

4300

AN:

1384236

Hom.:

Cov.:

AF XY:

0.00325

AC XY:

2217

AN XY:

683066

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00442

Gnomad4 ASJ exome

AF:

0.00981

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.00110

Gnomad4 FIN exome

AF:

0.0126

Gnomad4 NFE exome

AF:

0.00258

Gnomad4 OTH exome

AF:

0.00501

GnomAD4 genome

AF:

0.00736

AC:

1121

AN:

152226

Hom.:

Cov.:

AF XY:

0.00715

AC XY:

532

AN XY:

74420

show subpopulations

Gnomad4 AFR

AF:

0.00178

Gnomad4 AMR

AF:

0.0116

Gnomad4 ASJ

AF:

0.0159

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.0127

Gnomad4 NFE

AF:

0.00916

Gnomad4 OTH

AF:

0.0171

Alfa

AF:

0.00857

Hom.:

Bravo

AF:

0.00780

TwinsUK

AF:

0.00917

AC:

ALSPAC

AF:

0.00623

AC:

ESP6500AA

AF:

0.000723

AC:

ESP6500EA

AF:

0.0113

AC:

ExAC

AF:

0.00568

AC:

127

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 06, 2017	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.63

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0053

Eigen

Benign

-0.49

Eigen_PC

Benign

-0.71

FATHMM_MKL

Benign

0.0023

LIST_S2

Benign

0.64

MetaRNN

Benign

0.0057

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.69

PROVEAN

Benign

-1.8

REVEL

Benign

0.034

Sift

Benign

0.030

Sift4G

Pathogenic

0.0010

Polyphen

1.0

Vest4

0.074

MVP

0.067

ClinPred

0.024

GERP RS

1.6

Varity_R

0.089

gMVP

0.038

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