Variant chr20-62309283-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005560.6(LAMA5):c.*53C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 1,565,582 control chromosomes in the GnomAD database, including 6,120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.068 ( 488 hom., cov: 30)

Exomes 𝑓: 0.086 ( 5632 hom. )

Consequence

LAMA5
NM_005560.6 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.32

Variant links:

Genes affected

LAMA5 (HGNC:6485): (laminin subunit alpha 5) This gene encodes one of the vertebrate laminin alpha chains. Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. The protein encoded by this gene is the alpha-5 subunit of of laminin-10 (laminin-511), laminin-11 (laminin-521) and laminin-15 (laminin-523). [provided by RefSeq, Jun 2013]

LAMA5 links:

LAMA5 (HGNC:):

LAMA5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 20-62309283-G-A is Benign according to our data. Variant chr20-62309283-G-A is described in ClinVar as [Benign]. Clinvar id is 1181666.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LAMA5	NM_005560.6 linkuse as main transcript	c.*53C>T		3_prime_UTR_variant	80/80	ENST00000252999.7	NP_005551.3	O15230-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
LAMA5	ENST00000252999 linkuse as main transcript	c.*53C>T	3_prime_UTR_variant	80/80	1	NM_005560.6	ENSP00000252999.3	O15230-1
LAMA5	ENST00000370691.6 linkuse as main transcript	n.2936C>T	non_coding_transcript_exon_variant	17/17	1
LAMA5	ENST00000495695.1 linkuse as main transcript	n.642C>T	non_coding_transcript_exon_variant	4/4	2
LAMA5	ENST00000492698.1 linkuse as main transcript	n.-26C>T	upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0683

AC:

10384

AN:

152074

Hom.:

489

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0179

Gnomad AMI

AF:

0.140

Gnomad AMR

AF:

0.0835

Gnomad ASJ

AF:

0.0986

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.0771

Gnomad FIN

AF:

0.0935

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0938

Gnomad OTH

AF:

0.0717

GnomAD4 exome

AF:

0.0864

AC:

122119

AN:

1413388

Hom.:

5632

Cov.:

AF XY:

0.0866

AC XY:

60714

AN XY:

700712

show subpopulations

Gnomad4 AFR exome

AF:

0.0137

Gnomad4 AMR exome

AF:

0.0908

Gnomad4 ASJ exome

AF:

0.101

Gnomad4 EAS exome

AF:

0.000973

Gnomad4 SAS exome

AF:

0.0781

Gnomad4 FIN exome

AF:

0.105

Gnomad4 NFE exome

AF:

0.0913

Gnomad4 OTH exome

AF:

0.0854

GnomAD4 genome

AF:

0.0682

AC:

10381

AN:

152194

Hom.:

488

Cov.:

AF XY:

0.0690

AC XY:

5133

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0179

Gnomad4 AMR

AF:

0.0832

Gnomad4 ASJ

AF:

0.0986

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.0773

Gnomad4 FIN

AF:

0.0935

Gnomad4 NFE

AF:

0.0938

Gnomad4 OTH

AF:

0.0704

Alfa

AF:

0.0682

Hom.:

139

Bravo

AF:

0.0654

Asia WGS

AF:

0.0330

AC:

113

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 14, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.19

DANN

Benign

0.70

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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