13-113316347-A-C

Variant names:

• chr13-113316347-A-C
• rs12871648
• NM_005561.4:c.563-3122A>C

Variant summary

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

The NM_005561.4(LAMP1):​c.563-3122A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 151,556 control chromosomes in the GnomAD database, including 6,503 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 0.29 (6503 hom., cov: 29)
• Consequence: LAMP1 NM_005561.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.480

Genes affected

LAMP1 (HGNC:6499): (lysosomal associated membrane protein 1) The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may also play a role in tumor cell metastasis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAMP1	NM_005561.4	c.563-3122A>C		intron_variant	Intron 4 of 8	ENST00000332556.5	NP_005552.3
LAMP1	XM_011537494.3	c.506-3122A>C		intron_variant	Intron 4 of 8		XP_011535796.1
LAMP1	XM_047430302.1	c.497-3122A>C		intron_variant	Intron 4 of 8		XP_047286258.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAMP1	ENST00000332556.5	c.563-3122A>C		intron_variant	Intron 4 of 8	1	NM_005561.4	ENSP00000333298.4
LAMP1	ENST00000472564.1	n.2055-3122A>C		intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43618 AN: 151450 Hom.: 6500 Cov.: 29

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.288 AC: 43637 AN: 151556 Hom.: 6503 Cov.: 29 AF XY: 0.284 AC XY: 21051 AN XY: 74020

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.289

Alfa AF: 0.321 Hom.: 10705

Bravo AF: 0.286

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.73

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: rs12871648; hg19: chr13-113970662;