Variant 11-1747678-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001170820.4(IFITM10):c.526T>A(p.Tyr176Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000243 in 1,399,364 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.000024 ( 0 hom. )

Consequence

IFITM10
NM_001170820.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.05

Variant links:

Genes affected

IFITM10 (HGNC:40022): (interferon induced transmembrane protein 10) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

IFITM10 links:

ENSG00000250644 (HGNC:):

ENSG00000250644 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.35788915).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFITM10	NM_001170820.4 linkuse as main transcript	c.526T>A	p.Tyr176Asn	missense_variant	2/3	ENST00000340134.5	NP_001164291.2	A6NMD0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFITM10	ENST00000340134.5 linkuse as main transcript	c.526T>A	p.Tyr176Asn	missense_variant	2/3	3	NM_001170820.4	ENSP00000344430.4		A6NMD0
ENSG00000250644	ENST00000636615.1 linkuse as main transcript	c.1513T>A	p.Tyr505Asn	missense_variant	9/10	5		ENSP00000490014.1		A0A1B0GU92

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.000215

AC:

AN:

153704

Hom.:

AF XY:

0.000122

AC XY:

AN XY:

81664

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00130

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000228

GnomAD4 exome

AF:

0.0000243

AC:

AN:

1399364

Hom.:

Cov.:

AF XY:

0.0000159

AC XY:

AN XY:

690214

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000953

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:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000642

ExAC

AF:

0.0000311

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

May 13, 2024

The c.526T>A (p.Y176N) alteration is located in exon 2 (coding exon 2) of the IFITM10 gene. This alteration results from a T to A substitution at nucleotide position 526, causing the tyrosine (Y) at amino acid position 176 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.99

BayesDel_addAF

Benign

-0.19

BayesDel_noAF

Uncertain

-0.080

CADD

Uncertain

DANN

Benign

0.96

DEOGEN2

Uncertain

0.71

D;.;.

Eigen

Benign

0.10

Eigen_PC

Benign

0.094

FATHMM_MKL

Uncertain

0.83

LIST_S2

Pathogenic

0.98

D;D;D

M_CAP

Pathogenic

0.79

MetaRNN

Benign

0.36

T;T;T

MetaSVM

Uncertain

0.19

MutationAssessor

Benign

1.5

L;.;.

PrimateAI

Pathogenic

0.86

PROVEAN

Pathogenic

-7.8

D;.;.

REVEL

Pathogenic

0.67

Sift

Uncertain

0.019

D;.;.

Sift4G

Uncertain

0.0040

D;.;.

Vest4

0.92

MutPred

0.84

Gain of disorder (P = 0.0727);.;.;

MVP

0.63

ClinPred

0.27

GERP RS

2.3

Varity_R

0.55

gMVP

0.95

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