rs3795438

Variant names:

• chr1-30733790-C-T
• rs3795438
• NM_006762.3:c.*38G>A

Variant summary

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

The NM_006762.3(LAPTM5):​c.*38G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 1,589,694 control chromosomes in the GnomAD database, including 46,042 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 0.18 (3061 hom., cov: 33)
  • Exomes 𝑓: 0.24 (42981 hom.)
• Consequence: LAPTM5 NM_006762.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760
• Publications: 15 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006762.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAPTM5	NM_006762.3	MANE Select	c.*38G>A		3_prime_UTR	Exon 8 of 8	NP_006753.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LAPTM5	ENST00000294507.4	TSL:1 MANE Select	c.*38G>A		3_prime_UTR	Exon 8 of 8	ENSP00000294507.3
	LAPTM5	ENST00000464569.1	TSL:5	n.*99G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26710 AN: 152120 Hom.: 3067 Cov.: 33

Gnomad AFR AF: 0.0460

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.0697

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.172

GnomAD2 exomes AF: 0.197 AC: 43294 AN: 220200 AF XY: 0.200

Gnomad AFR exome AF: 0.0411

Gnomad AMR exome AF: 0.104

Gnomad ASJ exome AF: 0.210

Gnomad EAS exome AF: 0.0808

Gnomad FIN exome AF: 0.297

Gnomad NFE exome AF: 0.258

Gnomad OTH exome AF: 0.209

GnomAD4 exome AF: 0.237 AC: 341330 AN: 1437456 Hom.: 42981 Cov.: 36 AF XY: 0.235 AC XY: 168019 AN XY: 713682

African (AFR) AF: 0.0392 AC: 1271 AN: 32386

American (AMR) AF: 0.108 AC: 4299 AN: 39818

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 5125 AN: 25324

East Asian (EAS) AF: 0.0819 AC: 3211 AN: 39226

South Asian (SAS) AF: 0.151 AC: 12627 AN: 83852

European-Finnish (FIN) AF: 0.287 AC: 14224 AN: 49534

Middle Eastern (MID) AF: 0.179 AC: 1010 AN: 5632

European-Non Finnish (NFE) AF: 0.260 AC: 286991 AN: 1102418

Other (OTH) AF: 0.212 AC: 12572 AN: 59266

GnomAD4 genome AF: 0.175 AC: 26702 AN: 152238 Hom.: 3061 Cov.: 33 AF XY: 0.173 AC XY: 12876 AN XY: 74412

African (AFR) AF: 0.0459 AC: 1908 AN: 41562

American (AMR) AF: 0.135 AC: 2071 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3468

East Asian (EAS) AF: 0.0699 AC: 362 AN: 5182

South Asian (SAS) AF: 0.126 AC: 606 AN: 4814

European-Finnish (FIN) AF: 0.294 AC: 3110 AN: 10592

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17303 AN: 68000

Other (OTH) AF: 0.170 AC: 360 AN: 2114

Alfa AF: 0.226 Hom.: 7193

Bravo AF: 0.159

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	17
DANN	Benign	0.91
PhyloP100		0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs3795438; hg19: chr1-31206637; COSMIC: COSV53853022; COSMIC: COSV53853022;