1-30751153-T-C

Variant summary

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

The NM_006762.3(LAPTM5):c.87+6506A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 152,192 control chromosomes in the GnomAD database, including 8,841 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 0.34 (8841 hom., cov: 34)
• Consequence: LAPTM5 NM_006762.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.814

Genes affected

LAPTM5 (HGNC:29612): (lysosomal protein transmembrane 5) This gene encodes a transmembrane receptor that is associated with lysosomes. The encoded protein, also known as E3 protein, may play a role in hematopoiesis. [provided by RefSeq, Feb 2009]

LOC105378620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LAPTM5	NM_006762.3	c.87+6506A>G		intron_variant		ENST00000294507.4
LOC105378620	XR_007065566.1	n.1208A>G		non_coding_transcript_exon_variant	1/2
LAPTM5	XM_011542098.3	c.87+6506A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LAPTM5	ENST00000294507.4	c.87+6506A>G		intron_variant		1	NM_006762.3	P1
LAPTM5	ENST00000476492.1	n.99+6506A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51231 AN: 152074 Hom.: 8833 Cov.: 34

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.337 AC: 51284 AN: 152192 Hom.: 8841 Cov.: 34 AF XY: 0.332 AC XY: 24685 AN XY: 74422

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.314

Alfa AF: 0.332 Hom.: 1033

Bravo AF: 0.335

Asia WGS AF: 0.358 AC: 1248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.4
Dann	Benign	0.21

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

Other links and lift over

dbSNP: rs1188348; hg19: chr1-31224000;