ENST00000440160.1:n.81+16953T>A

Variant names:

• chr13-34623652-A-T
• rs885170
• ENST00000440160.1:n.81+16953T>A

Variant summary

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

The ENST00000440160.1(LINC00457):​n.81+16953T>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: 30)
• Consequence: LINC00457 ENST00000440160.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 1 publications found

Genes affected

LINC00457 (HGNC:42805): (long intergenic non-protein coding RNA 457)

ENSG00000271901 (HGNC:):

LINC02343 (HGNC:53263): (long intergenic non-protein coding RNA 2343)

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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00457	NR_047036.1	n.81+16953T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00457	ENST00000440160.1	n.81+16953T>A		intron_variant	Intron 1 of 2	2
ENSG00000271901	ENST00000606365.1	n.183+47348T>A		intron_variant	Intron 1 of 1	5
LINC00457	ENST00000660916.1	n.199+16953T>A		intron_variant	Intron 1 of 2
LINC02343	ENST00000791005.1	n.251-1554A>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.053
DANN	Benign	0.46
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs885170; hg19: chr13-35197789;