Variant 1-152910324-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_005547.4(IVL):c.527C>T(p.Pro176Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000245 in 1,428,266 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. P176P) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.000049 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000025 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

IVL
NM_005547.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -2.13

Variant links:

Genes affected

IVL (HGNC:6187): (involucrin) Involucrin, a component of the keratinocyte crosslinked envelope, is found in the cytoplasm and crosslinked to membrane proteins by transglutaminase. This gene is mapped to 1q21, among calpactin I light chain, trichohyalin, profillaggrin, loricrin, and calcyclin. [provided by RefSeq, Jul 2008]

IVL links:

ENSG00000289062 (HGNC:):

ENSG00000289062 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.047594905).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IVL	NM_005547.4 linkuse as main transcript	c.527C>T	p.Pro176Leu	missense_variant	2/2	ENST00000368764.4	NP_005538.2	P07476

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IVL	ENST00000368764.4 linkuse as main transcript	c.527C>T	p.Pro176Leu	missense_variant	2/2	2	NM_005547.4	ENSP00000357753.3	P07476
ENSG00000289062	ENST00000686895.2 linkuse as main transcript	n.94+2717G>A		intron_variant
ENSG00000289062	ENST00000702923.1 linkuse as main transcript	n.238+2549G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

142578

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0000514

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000782

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000387

AC:

AN:

206698

Hom.:

AF XY:

0.0000720

AC XY:

AN XY:

111176

show subpopulations

Gnomad AFR exome

AF:

0.0000817

Gnomad AMR exome

AF:

0.00

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:

0.0000549

Gnomad OTH exome

AF:

0.000384

GnomAD4 exome

AF:

0.0000245

AC:

AN:

1428266

Hom.:

Cov.:

AF XY:

0.0000367

AC XY:

AN XY:

708108

show subpopulations

Gnomad4 AFR exome

AF:

0.0000304

Gnomad4 AMR exome

AF:

0.0000729

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000121

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000257

Gnomad4 OTH exome

AF:

0.0000340

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0000491

AC:

AN:

142708

Hom.:

Cov.:

AF XY:

0.0000286

AC XY:

AN XY:

69850

show subpopulations

Gnomad4 AFR

AF:

0.0000513

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000782

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000192

Hom.:

TwinsUK

AF:

0.00162

AC:

ALSPAC

AF:

0.00234

AC:

ExAC

AF:

0.0000417

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

Apr 07, 2022

The c.527C>T (p.P176L) alteration is located in exon 2 (coding exon 1) of the IVL gene. This alteration results from a C to T substitution at nucleotide position 527, causing the proline (P) at amino acid position 176 to be replaced by a leucine (L). 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

Benign

0.076

BayesDel_addAF

Benign

-0.61

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.15

DANN

Benign

0.21

DEOGEN2

Benign

0.049

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.0084

LIST_S2

Benign

0.46

M_CAP

Benign

0.0092

MetaRNN

Benign

0.048

MetaSVM

Benign

-0.91

MutationAssessor

Benign

1.4

PrimateAI

Benign

0.19

PROVEAN

Benign

-0.81

REVEL

Benign

0.014

Sift

Benign

0.32

Sift4G

Benign

0.24

Polyphen

0.11

Vest4

0.11

MVP

0.13

MPC

0.0048

ClinPred

0.015

GERP RS

-4.3

Varity_R

0.033

gMVP

0.0080

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