10-108428634-T-G

Variant names:

• chr10-108428634-T-G
• rs9332405
• ENST00000809134.1:n.158+1088A>C

Variant summary

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

The ENST00000809134.1(LINC01435):​n.158+1088A>C 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: 31)
• Consequence: LINC01435 ENST00000809134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 3 publications found

Genes affected

LINC01435 (HGNC:50753): (long intergenic non-protein coding RNA 1435)

LOC105378477 (HGNC:):

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=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378477	XR_946308.2	n.911+21336A>C		intron_variant	Intron 3 of 4
LOC105378477	XR_946309.2	n.634+21336A>C		intron_variant	Intron 3 of 4
LOC105378477	XR_946310.2	n.613+21336A>C		intron_variant	Intron 3 of 4
LOC105378477	XR_946312.2	n.912-7152A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01435	ENST00000809134.1	n.158+1088A>C		intron_variant	Intron 1 of 3
LINC01435	ENST00000809136.1	n.540+21336A>C		intron_variant	Intron 3 of 4
LINC01435	ENST00000809137.1	n.541-7152A>C		intron_variant	Intron 3 of 3
LINC01435	ENST00000809138.1	n.144+1088A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.31
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs9332405; hg19: chr10-110188392;