ENST00000849543.1:n.164A>G

Variant names:

• chr2-20060751-T-C
• rs11694170
• ENST00000849543.1:n.164A>G

Variant summary

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

The ENST00000849543.1(ENSG00000310395):​n.164A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,224 control chromosomes in the GnomAD database, including 2,556 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 0.16 (2556 hom., cov: 33)
• Consequence: ENSG00000310395 ENST00000849543.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 4 publications found

Genes affected

ENSG00000310395 (HGNC:):

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849543.1. 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
	LAPTM4A-DT	NR_187142.1		n.359-1030T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310395	ENST00000849543.1		n.164A>G		splice_region non_coding_transcript_exon	Exon 2 of 3
	LAPTM4A-DT	ENST00000452342.4	TSL:2	n.647-5765T>C		intron	N/A
	LAPTM4A-DT	ENST00000849369.1		n.358+8257T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24447 AN: 152108 Hom.: 2553 Cov.: 33

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0928

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.161 AC: 24459 AN: 152224 Hom.: 2556 Cov.: 33 AF XY: 0.167 AC XY: 12421 AN XY: 74404

African (AFR) AF: 0.0404 AC: 1679 AN: 41572

American (AMR) AF: 0.176 AC: 2690 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0928 AC: 322 AN: 3468

East Asian (EAS) AF: 0.306 AC: 1580 AN: 5160

South Asian (SAS) AF: 0.216 AC: 1039 AN: 4820

European-Finnish (FIN) AF: 0.285 AC: 3023 AN: 10594

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13664 AN: 67996

Other (OTH) AF: 0.149 AC: 314 AN: 2114

Alfa AF: 0.188 Hom.: 1564

Bravo AF: 0.145

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.72
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs11694170; hg19: chr2-20260512;