1-30742517-T-C

Variant names:

• chr1-30742517-T-C
• rs1050663
• NM_006762.3:c.120A>G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_006762.3(LAPTM5):​c.120A>G​(p.Ser40Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 1,612,044 control chromosomes in the GnomAD database, including 217,685 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 0.55 (23304 hom., cov: 32)
  • Exomes 𝑓: 0.51 (194381 hom.)
• Consequence: LAPTM5 NM_006762.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.21

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

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP7: Synonymous conserved (PhyloP=-5.21 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAPTM5	NM_006762.3	c.120A>G	p.Ser40Ser	synonymous_variant	Exon 2 of 8	ENST00000294507.4	NP_006753.1
LAPTM5	XM_011542098.3	c.88-2580A>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.120A>G	p.Ser40Ser	synonymous_variant	Exon 2 of 8	1	NM_006762.3	ENSP00000294507.3
LAPTM5	ENST00000464569.1	n.345A>G		non_coding_transcript_exon_variant	Exon 2 of 8	5
LAPTM5	ENST00000476492.1	n.132A>G		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83528 AN: 151942 Hom.: 23273 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.542

GnomAD3 exomes AF: 0.556 AC: 138954 AN: 249732 Hom.: 39848 AF XY: 0.547 AC XY: 73787 AN XY: 134994

Gnomad AFR exome AF: 0.603

Gnomad AMR exome AF: 0.729

Gnomad ASJ exome AF: 0.483

Gnomad EAS exome AF: 0.693

Gnomad SAS exome AF: 0.540

Gnomad FIN exome AF: 0.583

Gnomad NFE exome AF: 0.483

Gnomad OTH exome AF: 0.527

GnomAD4 exome AF: 0.511 AC: 746647 AN: 1459984 Hom.: 194381 Cov.: 41 AF XY: 0.511 AC XY: 371022 AN XY: 726274

Gnomad4 AFR exome AF: 0.602

Gnomad4 AMR exome AF: 0.719

Gnomad4 ASJ exome AF: 0.479

Gnomad4 EAS exome AF: 0.722

Gnomad4 SAS exome AF: 0.539

Gnomad4 FIN exome AF: 0.569

Gnomad4 NFE exome AF: 0.488

Gnomad4 OTH exome AF: 0.523

GnomAD4 genome AF: 0.550 AC: 83607 AN: 152060 Hom.: 23304 Cov.: 32 AF XY: 0.555 AC XY: 41272 AN XY: 74346

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.647

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.546

Alfa AF: 0.506 Hom.: 25219

Bravo AF: 0.561

Asia WGS AF: 0.620 AC: 2155 AN: 3478

EpiCase AF: 0.488

EpiControl AF: 0.487

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1050663; hg19: chr1-31215364;