16-58443471-G-T

Variant names:

• chr16-58443471-G-T
• rs1862802
• ENST00000561906.5:n.215+7648G>T

Variant summary

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

The ENST00000561906.5(LINC02137):​n.215+7648G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 151,940 control chromosomes in the GnomAD database, including 27,248 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 0.58 (27248 hom., cov: 31)
• Consequence: LINC02137 ENST00000561906.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 8 publications found

Genes affected

LINC02137 (HGNC:52997): (long intergenic non-protein coding RNA 2137)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561906.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02137	NR_187253.1		n.228+7648G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02137	ENST00000561906.5	TSL:3	n.215+7648G>T		intron	N/A
	LINC02137	ENST00000567448.1	TSL:5	n.297-6591G>T		intron	N/A
	LINC02137	ENST00000725711.1		n.422-7304G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87389 AN: 151824 Hom.: 27186 Cov.: 31

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.576 AC: 87517 AN: 151940 Hom.: 27248 Cov.: 31 AF XY: 0.581 AC XY: 43135 AN XY: 74208

African (AFR) AF: 0.824 AC: 34176 AN: 41468

American (AMR) AF: 0.602 AC: 9194 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1311 AN: 3466

East Asian (EAS) AF: 0.605 AC: 3128 AN: 5166

South Asian (SAS) AF: 0.561 AC: 2699 AN: 4808

European-Finnish (FIN) AF: 0.494 AC: 5197 AN: 10512

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30169 AN: 67928

Other (OTH) AF: 0.525 AC: 1108 AN: 2112

Alfa AF: 0.460 Hom.: 8937

Bravo AF: 0.593

Asia WGS AF: 0.613 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.0
DANN	Benign	0.81
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs1862802; hg19: chr16-58477375;