ENST00000733117.1:n.136+5444A>T

Variant names:

• chr4-36492983-T-A
• rs6850219
• ENST00000733117.1:n.136+5444A>T

Variant summary

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

The ENST00000733117.1(LINC02505):​n.136+5444A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,134 control chromosomes in the GnomAD database, including 1,668 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 0.10 (1668 hom., cov: 32)
• Consequence: LINC02505 ENST00000733117.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 1 publications found

Genes affected

LINC02505 (HGNC:53494): (long intergenic non-protein coding RNA 2505)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733117.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02505	ENST00000733117.1		n.136+5444A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15939 AN: 152016 Hom.: 1673 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0237

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.105 AC: 15952 AN: 152134 Hom.: 1668 Cov.: 32 AF XY: 0.104 AC XY: 7700 AN XY: 74394

African (AFR) AF: 0.259 AC: 10756 AN: 41472

American (AMR) AF: 0.142 AC: 2168 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0237 AC: 82 AN: 3466

East Asian (EAS) AF: 0.108 AC: 558 AN: 5178

South Asian (SAS) AF: 0.0149 AC: 72 AN: 4832

European-Finnish (FIN) AF: 0.00396 AC: 42 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0306 AC: 2079 AN: 67996

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0712 Hom.: 118

Bravo AF: 0.124

Asia WGS AF: 0.0820 AC: 285 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs6850219; hg19: chr4-36494605;