ENST00000849372.1:n.502G>A

Variant names:

• chr2-20061924-G-A
• rs7565124
• ENST00000849372.1:n.502G>A

Variant summary

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

The ENST00000849372.1(LAPTM4A-DT):​n.502G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,112 control chromosomes in the GnomAD database, including 6,705 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 (6705 hom., cov: 33)
• Consequence: LAPTM4A-DT ENST00000849372.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 5 publications found

Genes affected

LAPTM4A-DT (HGNC:54382): (LAPTM4A divergent transcript)

ENSG00000310395 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAPTM4A-DT	NR_187142.1	n.502G>A		non_coding_transcript_exon_variant	Exon 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LAPTM4A-DT	ENST00000849372.1	n.502G>A		non_coding_transcript_exon_variant	Exon 2 of 3
LAPTM4A-DT	ENST00000849373.1	n.507G>A		non_coding_transcript_exon_variant	Exon 2 of 3
LAPTM4A-DT	ENST00000849374.1	n.519G>A		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44639 AN: 151994 Hom.: 6697 Cov.: 33

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.325

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.294 AC: 44663 AN: 152112 Hom.: 6705 Cov.: 33 AF XY: 0.290 AC XY: 21571 AN XY: 74378

African (AFR) AF: 0.326 AC: 13535 AN: 41486

American (AMR) AF: 0.287 AC: 4389 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1097 AN: 3472

East Asian (EAS) AF: 0.126 AC: 650 AN: 5156

South Asian (SAS) AF: 0.196 AC: 948 AN: 4828

European-Finnish (FIN) AF: 0.278 AC: 2939 AN: 10576

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.296 AC: 20100 AN: 67980

Other (OTH) AF: 0.299 AC: 631 AN: 2110

Alfa AF: 0.288 Hom.: 11913

Bravo AF: 0.300

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.32

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7565124; hg19: chr2-20261685;