rs382131

Variant names:

• chr7-108092844-G-C
• rs382131
• NM_007356.3:c.1471-428C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007356.3(LAMB4):​c.1471-428C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,858 control chromosomes in the GnomAD database, including 12,332 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (12332 hom., cov: 31)
• Consequence: LAMB4 NM_007356.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 1 publications found

Genes affected

LAMB4 (HGNC:6491): (laminin subunit beta 4) Predicted to be an extracellular matrix structural constituent. Predicted to be involved in several processes, including basement membrane assembly; cell migration; and substrate adhesion-dependent cell spreading. Predicted to be located in basement membrane; extracellular region; and membrane. Predicted to be part of laminin complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAMB4	NM_007356.3	c.1471-428C>G		intron_variant	Intron 12 of 33	ENST00000388781.8	NP_031382.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMB4	ENST00000388781.8	c.1471-428C>G		intron_variant	Intron 12 of 33	1	NM_007356.3	ENSP00000373433.3
LAMB4	ENST00000205386.8	c.1471-428C>G		intron_variant	Intron 12 of 33	1		ENSP00000205386.4
LAMB4	ENST00000418464.1	c.1471-428C>G		intron_variant	Intron 12 of 17	1		ENSP00000402353.2
LAMB4	ENST00000475469.1	n.1555-428C>G		intron_variant	Intron 12 of 22	2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60304 AN: 151740 Hom.: 12318 Cov.: 31

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.363

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.398 AC: 60364 AN: 151858 Hom.: 12332 Cov.: 31 AF XY: 0.403 AC XY: 29910 AN XY: 74214

African (AFR) AF: 0.370 AC: 15335 AN: 41404

American (AMR) AF: 0.470 AC: 7184 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1040 AN: 3472

East Asian (EAS) AF: 0.582 AC: 2975 AN: 5112

South Asian (SAS) AF: 0.367 AC: 1768 AN: 4820

European-Finnish (FIN) AF: 0.433 AC: 4567 AN: 10548

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26331 AN: 67922

Other (OTH) AF: 0.366 AC: 772 AN: 2110

Alfa AF: 0.396 Hom.: 1471

Bravo AF: 0.397

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.64
DANN	Benign	0.20
PhyloP100		-0.26
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs382131; hg19: chr7-107733289;