1-30751153-T-C

Variant names:

• chr1-30751153-T-C
• rs1188348
• NM_006762.3:c.87+6506A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LAPTM5	NM_006762.3	c.87+6506A>G		intron_variant	Intron 1 of 7	ENST00000294507.4	NP_006753.1
LOC105378620	XR_007065566.1	n.1208A>G		non_coding_transcript_exon_variant	Exon 1 of 2
LAPTM5	XM_011542098.3	c.87+6506A>G		intron_variant	Intron 1 of 5		XP_011540400.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAPTM5	ENST00000294507.4	c.87+6506A>G		intron_variant	Intron 1 of 7	1	NM_006762.3	ENSP00000294507.3
LAPTM5	ENST00000476492.1	n.99+6506A>G		intron_variant	Intron 1 of 1	2
ENSG00000309098	ENST00000838594.1	n.142+1045A>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.378 AC: 15704 AN: 41526

American (AMR) AF: 0.246 AC: 3760 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1778 AN: 5170

South Asian (SAS) AF: 0.391 AC: 1887 AN: 4828

European-Finnish (FIN) AF: 0.260 AC: 2761 AN: 10604

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23139 AN: 67974

Other (OTH) AF: 0.314 AC: 665 AN: 2116

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
PhyloP100		-0.81
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: rs1188348; hg19: chr1-31224000;