1-72744134-G-T

Variant names:

• chr1-72744134-G-T
• rs10493509
• ENST00000654386.1:n.436+5032C>A

Variant summary

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

The ENST00000654386.1(ENSG00000225087):​n.436+5032C>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: 32)
• Consequence: ENSG00000225087 ENST00000654386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440
• Publications: 1 publications found

Genes affected

ENSG00000225087 (HGNC:):

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

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=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378798	NR_188684.1	n.202+5032C>A		intron_variant	Intron 2 of 4
LOC105378798	NR_188685.1	n.230+5032C>A		intron_variant	Intron 3 of 4
LOC105378798	NR_188686.1	n.202+5032C>A		intron_variant	Intron 2 of 3
LOC105378798	NR_188687.1	n.202+5032C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225087	ENST00000654386.1	n.436+5032C>A		intron_variant	Intron 3 of 3
ENSG00000225087	ENST00000660076.1	n.207+5032C>A		intron_variant	Intron 2 of 2
ENSG00000225087	ENST00000661739.1	n.202+5032C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 57

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.44
PhyloP100		0.044

Splicing

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

Other links and lift over

dbSNP: rs10493509; hg19: chr1-73209817;