ENST00000603877.1:n.1723+620C>T

Variant names:

• chr3-49141557-G-A
• rs9880088
• ENST00000603877.1:n.1723+620C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000603877.1(LAMB2P1):​n.1723+620C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0937 in 151,918 control chromosomes in the GnomAD database, including 743 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 0.094 (743 hom., cov: 32)
• Consequence: LAMB2P1 ENST00000603877.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

Genes affected

LAMB2P1 (HGNC:6488): (laminin subunit beta 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMB2P1	ENST00000603877.1	n.1723+620C>T		intron_variant	Intron 13 of 13	6

Frequencies

GnomAD3 genomes AF: 0.0938 AC: 14239 AN: 151800 Hom.: 743 Cov.: 32

Gnomad AFR AF: 0.0837

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0356

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.0937 AC: 14240 AN: 151918 Hom.: 743 Cov.: 32 AF XY: 0.0933 AC XY: 6924 AN XY: 74216

Gnomad4 AFR AF: 0.0834

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0358

Gnomad4 SAS AF: 0.0622

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.0967

Alfa AF: 0.0988 Hom.: 389

Bravo AF: 0.0900

Asia WGS AF: 0.0540 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9880088; hg19: chr3-49178990;