13-65907683-G-T

Variant names:

• chr13-65907683-G-T
• rs1585440
• ENST00000663858.2:n.236+3457G>T

Variant summary

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

The ENST00000663858.2(LINC01052):​n.236+3457G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,938 control chromosomes in the GnomAD database, including 6,741 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 (6741 hom., cov: 32)
• Consequence: LINC01052 ENST00000663858.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232
• Publications: 16 publications found

Genes affected

LINC01052 (HGNC:49046): (long intergenic non-protein coding RNA 1052)

ENSG00000300318 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663858.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01052	ENST00000663858.2		n.236+3457G>T		intron	N/A
	LINC01052	ENST00000665754.1		n.193+3457G>T		intron	N/A
	ENSG00000300318	ENST00000770902.1		n.234+43010C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43497 AN: 151818 Hom.: 6730 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.286 AC: 43518 AN: 151938 Hom.: 6741 Cov.: 32 AF XY: 0.286 AC XY: 21279 AN XY: 74276

African (AFR) AF: 0.156 AC: 6479 AN: 41468

American (AMR) AF: 0.281 AC: 4293 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3464

East Asian (EAS) AF: 0.273 AC: 1406 AN: 5156

South Asian (SAS) AF: 0.414 AC: 1995 AN: 4822

European-Finnish (FIN) AF: 0.337 AC: 3555 AN: 10546

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.349 AC: 23705 AN: 67918

Other (OTH) AF: 0.293 AC: 616 AN: 2102

Alfa AF: 0.334 Hom.: 31254

Bravo AF: 0.276

Asia WGS AF: 0.356 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.76
DANN	Benign	0.15
PhyloP100		0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1585440;

hg19: chr13-66481815;