rs7698161

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-136887774-C-A
• chr4-136887774-C-G
• chr4-136887774-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000505736.5(LINC02511):​n.155+28401G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: LINC02511 ENST00000505736.5 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02511	NR_149105.1	n.155+28401G>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02511	ENST00000505736.5	n.155+28401G>T		intron_variant	Intron 3 of 3	5
LINC02511	ENST00000512039.1	n.93+28401G>T		intron_variant	Intron 2 of 3	3
LINC02511	ENST00000652184.1	n.240-74043G>T		intron_variant	Intron 4 of 5
LINC02511	ENST00000656956.1	n.129+28401G>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.69
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs7698161; hg19: chr4-137808928;