Variant 16-8885239-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate

The NM_001395433.1(LITAFD):c.163G>T(p.Val55Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000135 in 398,708 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 5/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.00024 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000069 ( 0 hom. )

Consequence

LITAFD
NM_001395433.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.04

Variant links:

Genes affected

LITAFD (HGNC:53927): (LITAF domain containing) Predicted to enable metal ion binding activity. Predicted to be located in lysosomal membrane. [provided by Alliance of Genome Resources, Apr 2022]

LITAFD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.28229505).

BP6

Variant 16-8885239-G-T is Benign according to our data. Variant chr16-8885239-G-T is described in ClinVar as [Benign]. Clinvar id is 2646184.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LITAFD	NM_001395433.1 linkuse as main transcript	c.163G>T	p.Val55Leu	missense_variant	4/4	ENST00000636296.2	NP_001382362.1
LITAFD	NM_001395434.1 linkuse as main transcript	c.163G>T	p.Val55Leu	missense_variant	4/4		NP_001382363.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LITAFD	ENST00000636296.2 linkuse as main transcript	c.163G>T	p.Val55Leu	missense_variant	4/4	5	NM_001395433.1	ENSP00000490685	P1
LITAFD	ENST00000637237.1 linkuse as main transcript	c.163G>T	p.Val55Leu	missense_variant	4/4	5		ENSP00000490446	P1

Frequencies

GnomAD3 genomes

AF:

0.000243

AC:

AN:

152038

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00210

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000294

Gnomad OTH

AF:

0.000478

GnomAD4 exome

AF:

0.0000690

AC:

AN:

246550

Hom.:

Cov.:

AF XY:

0.0000880

AC XY:

AN XY:

124966

show subpopulations

Gnomad4 AFR exome

AF:

0.000139

Gnomad4 AMR exome

AF:

0.000135

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000823

Gnomad4 OTH exome

AF:

0.000122

GnomAD4 genome

AF:

0.000243

AC:

AN:

152158

Hom.:

Cov.:

AF XY:

0.000336

AC XY:

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.0000241

Gnomad4 AMR

AF:

0.00209

Gnomad4 ASJ

AF:

0.000290

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000294

Gnomad4 OTH

AF:

0.000473

Bravo

AF:

0.000332

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

USP7: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.31

BayesDel_noAF

Benign

-0.52

CADD

Benign

DANN

Benign

0.81

FATHMM_MKL

Uncertain

0.83

LIST_S2

Benign

0.56

.;T

MetaRNN

Benign

0.28

T;T

GERP RS

3.4

Splicing

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