Variant 1-201386876-ACC-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_005558.4(LAD1):c.483_484del(p.Leu161PhefsTer31) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0336 in 1,379,396 control chromosomes in the GnomAD database, including 1,771 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.067 ( 482 hom., cov: 30)

Exomes 𝑓: 0.030 ( 1289 hom. )

Consequence

LAD1
NM_005558.4 frameshift

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0920

Variant links:

Genes affected

LAD1 (HGNC:6472): (ladinin 1) The protein encoded by this gene may be an anchoring filament that is a component of basement membranes. It may contribute to the stability of the association of the epithelial layers with the underlying mesenchyme. [provided by RefSeq, Jul 2008]

LAD1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 1-201386876-ACC-A is Benign according to our data. Variant chr1-201386876-ACC-A is described in ClinVar as [Benign]. Clinvar id is 780294.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LAD1	NM_005558.4 linkuse as main transcript	c.483_484del	p.Leu161PhefsTer31	frameshift_variant	3/10	ENST00000391967.7	NP_005549.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LAD1	ENST00000391967.7 linkuse as main transcript	c.483_484del	p.Leu161PhefsTer31	frameshift_variant	3/10	1	NM_005558.4	ENSP00000375829	P3

Frequencies

GnomAD3 genomes

AF:

0.0669

AC:

8922

AN:

133392

Hom.:

483

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0265

Gnomad ASJ

AF:

0.0224

Gnomad EAS

AF:

0.0532

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0756

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0169

Gnomad OTH

AF:

0.0485

GnomAD4 exome

AF:

0.0301

AC:

37452

AN:

1245900

Hom.:

1289

AF XY:

0.0323

AC XY:

20083

AN XY:

621416

show subpopulations

Gnomad4 AFR exome

AF:

0.172

Gnomad4 AMR exome

AF:

0.0167

Gnomad4 ASJ exome

AF:

0.0244

Gnomad4 EAS exome

AF:

0.0548

Gnomad4 SAS exome

AF:

0.109

Gnomad4 FIN exome

AF:

0.0792

Gnomad4 NFE exome

AF:

0.0158

Gnomad4 OTH exome

AF:

0.0384

GnomAD4 genome

AF:

0.0669

AC:

8931

AN:

133496

Hom.:

482

Cov.:

AF XY:

0.0691

AC XY:

4536

AN XY:

65674

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.0264

Gnomad4 ASJ

AF:

0.0224

Gnomad4 EAS

AF:

0.0533

Gnomad4 SAS

AF:

0.120

Gnomad4 FIN

AF:

0.0756

Gnomad4 NFE

AF:

0.0169

Gnomad4 OTH

AF:

0.0483

Alfa

AF:

0.0238

Hom.:

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

Labcorp Genetics (formerly Invitae), Labcorp

Aug 27, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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