4-173957277-C-T

Variant names:

• chr4-173957277-C-T
• rs10588631
• ENST00000511291.1:n.146-29287G>A

Variant summary

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

The ENST00000511291.1(ENSG00000251216):​n.146-29287G>A 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: 21)
• Consequence: ENSG00000251216 ENST00000511291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.13
• Publications: 0 publications found

Genes affected

ENSG00000251216 (HGNC:):

LINC02269 (HGNC:53184): (long intergenic non-protein coding RNA 2269)

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=-1.08).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511291.1. 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
	LOC105377543	NR_188466.1		n.365-19914G>A		intron	N/A
	LOC105377543	NR_188467.1		n.261-19914G>A		intron	N/A
	LOC105377543	NR_188468.1		n.261-19914G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251216	ENST00000511291.1	TSL:3	n.146-29287G>A		intron	N/A
	LINC02269	ENST00000656853.1		n.641+1228C>T		intron	N/A
	ENSG00000251216	ENST00000662648.2		n.423-19914G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 21

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

GnomAD4 genome Cov.: 21

Alfa AF: 0.00 Hom.: 1118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0020
DANN	Benign	0.34
PhyloP100		-7.1

Splicing

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

Other links and lift over

dbSNP: rs10588631; hg19: chr4-174878428;