16-58443471-G-T

Position:

• chr16-58443471-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02137 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02137	NR_187253.1	n.228+7648G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02137	ENST00000561906.5	n.215+7648G>T		intron_variant		3
LINC02137	ENST00000567448.1	n.297-6591G>T		intron_variant		5

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

Gnomad4 AFR AF: 0.824

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.494

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.525

Alfa AF: 0.457 Hom.: 7859

Bravo AF: 0.593

Asia WGS AF: 0.613 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1862802; hg19: chr16-58477375;