chr2-20056431-G-A

Variant names:

• chr2-20056431-G-A
• rs12471796
• NR_187142.1:n.358+3937G>A

Variant summary

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

The NR_187142.1(LAPTM4A-DT):​n.358+3937G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,812 control chromosomes in the GnomAD database, including 6,595 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 (6595 hom., cov: 32)
• Consequence: LAPTM4A-DT NR_187142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320

Genes affected

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LAPTM4A-DT	NR_187142.1	n.358+3937G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44412 AN: 151694 Hom.: 6587 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.293 AC: 44435 AN: 151812 Hom.: 6595 Cov.: 32 AF XY: 0.289 AC XY: 21446 AN XY: 74210

African (AFR) AF: 0.325 AC: 13459 AN: 41392

American (AMR) AF: 0.286 AC: 4366 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3466

East Asian (EAS) AF: 0.127 AC: 659 AN: 5180

South Asian (SAS) AF: 0.195 AC: 943 AN: 4826

European-Finnish (FIN) AF: 0.276 AC: 2900 AN: 10502

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20016 AN: 67866

Other (OTH) AF: 0.298 AC: 627 AN: 2106

Alfa AF: 0.298 Hom.: 19217

Bravo AF: 0.300

Asia WGS AF: 0.178 AC: 621 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12471796; hg19: chr2-20256192;