chr4-136887774-C-T

Variant names:

• chr4-136887774-C-T
• rs7698161
• ENST00000505736.5:n.155+28401G>A

Variant summary

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

The ENST00000512039.1(LINC02511):​n.93+28401G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,960 control chromosomes in the GnomAD database, including 11,410 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 0.38 (11410 hom., cov: 33)
• Consequence: LINC02511 ENST00000512039.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 2 publications found

Genes affected

LINC02511 (HGNC:53500): (long intergenic non-protein coding RNA 2511)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512039.1. 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
	LINC02511	NR_149105.1		n.155+28401G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02511	ENST00000505736.5	TSL:5	n.155+28401G>A		intron	N/A
	LINC02511	ENST00000512039.1	TSL:3	n.93+28401G>A		intron	N/A
	LINC02511	ENST00000652184.1		n.240-74043G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58460 AN: 151842 Hom.: 11396 Cov.: 33

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.385 AC: 58501 AN: 151960 Hom.: 11410 Cov.: 33 AF XY: 0.385 AC XY: 28602 AN XY: 74270

African (AFR) AF: 0.390 AC: 16154 AN: 41468

American (AMR) AF: 0.427 AC: 6511 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1008 AN: 3468

East Asian (EAS) AF: 0.548 AC: 2826 AN: 5158

South Asian (SAS) AF: 0.386 AC: 1860 AN: 4818

European-Finnish (FIN) AF: 0.365 AC: 3849 AN: 10552

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25086 AN: 67936

Other (OTH) AF: 0.394 AC: 832 AN: 2112

Alfa AF: 0.374 Hom.: 33695

Bravo AF: 0.392

Asia WGS AF: 0.447 AC: 1553 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.025

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: rs7698161;

hg19: chr4-137808928;