Variant 17-32931668-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_015544.3(TMEM98):c.131+9G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,603,584 control chromosomes in the GnomAD database, including 3,365 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.047 ( 235 hom., cov: 32)

Exomes 𝑓: 0.061 ( 3130 hom. )

Consequence

TMEM98
NM_015544.3 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -2.03

Variant links:

Genes affected

TMEM98 (HGNC:24529): (transmembrane protein 98) This gene encodes a transmembrane protein. A missense mutation in this gene result in Nanophthalmos 4 (NNO4). Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2014]

TMEM98 links:

TMEM98 (HGNC:):

TMEM98 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.79).

BP6

Variant 17-32931668-G-C is Benign according to our data. Variant chr17-32931668-G-C is described in ClinVar as [Benign]. Clinvar id is 3059403.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.071 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
TMEM98	NM_015544.3 linkuse as main transcript	c.131+9G>C	intron_variant	ENST00000579849.6	NP_056359.2	Q9Y2Y6
TMEM98	NM_001033504.2 linkuse as main transcript	c.131+9G>C	intron_variant		NP_001028676.1	Q9Y2Y6
TMEM98	NM_001301746.2 linkuse as main transcript	c.131+9G>C	intron_variant		NP_001288675.1	Q9Y2Y6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM98	ENST00000579849.6 linkuse as main transcript	c.131+9G>C		intron_variant		1	NM_015544.3	ENSP00000463245.1		Q9Y2Y6

Frequencies

GnomAD3 genomes

AF:

0.0471

AC:

7173

AN:

152170

Hom.:

234

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0128

Gnomad AMI

AF:

0.0998

Gnomad AMR

AF:

0.0455

Gnomad ASJ

AF:

0.0904

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0215

Gnomad FIN

AF:

0.0336

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0727

Gnomad OTH

AF:

0.0508

GnomAD3 exomes

AF:

0.0491

AC:

11287

AN:

230076

Hom.:

381

AF XY:

0.0495

AC XY:

6126

AN XY:

123718

show subpopulations

Gnomad AFR exome

AF:

0.0121

Gnomad AMR exome

AF:

0.0377

Gnomad ASJ exome

AF:

0.0825

Gnomad EAS exome

AF:

0.0000578

Gnomad SAS exome

AF:

0.0193

Gnomad FIN exome

AF:

0.0329

Gnomad NFE exome

AF:

0.0724

Gnomad OTH exome

AF:

0.0748

GnomAD4 exome

AF:

0.0613

AC:

88978

AN:

1451296

Hom.:

3130

Cov.:

AF XY:

0.0606

AC XY:

43647

AN XY:

720522

show subpopulations

Gnomad4 AFR exome

AF:

0.0102

Gnomad4 AMR exome

AF:

0.0390

Gnomad4 ASJ exome

AF:

0.0868

Gnomad4 EAS exome

AF:

0.000152

Gnomad4 SAS exome

AF:

0.0207

Gnomad4 FIN exome

AF:

0.0360

Gnomad4 NFE exome

AF:

0.0697

Gnomad4 OTH exome

AF:

0.0570

GnomAD4 genome

AF:

0.0471

AC:

7169

AN:

152288

Hom.:

235

Cov.:

AF XY:

0.0453

AC XY:

3374

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.0127

Gnomad4 AMR

AF:

0.0454

Gnomad4 ASJ

AF:

0.0904

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0216

Gnomad4 FIN

AF:

0.0336

Gnomad4 NFE

AF:

0.0727

Gnomad4 OTH

AF:

0.0507

Alfa

AF:

0.0555

Hom.:

Bravo

AF:

0.0484

Asia WGS

AF:

0.0130

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

TMEM98-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 03, 2020

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.039

DANN

Benign

0.75

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