chr14-97940088-A-G

Variant names:

• chr14-97940088-A-G
• rs2809115
• ENST00000499006.8:n.436-13444T>C

Variant summary

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

The ENST00000499006.8(LINC01550):​n.436-13444T>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: 32)
• Consequence: LINC01550 ENST00000499006.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 4 publications found

Genes affected

LINC01550 (HGNC:20111): (long intergenic non-protein coding RNA 1550)

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=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01550	NR_015430.2	n.424-13444T>C		intron_variant	Intron 2 of 2
LINC01550	NR_152749.1	n.424-5207T>C		intron_variant	Intron 2 of 2
LINC01550	NR_152750.1	n.347-5207T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01550	ENST00000499006.8	n.436-13444T>C		intron_variant	Intron 2 of 2	1
LINC01550	ENST00000556462.1	n.279-5207T>C		intron_variant	Intron 2 of 2	2
LINC01550	ENST00000652825.1	n.365-5207T>C		intron_variant	Intron 2 of 2

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

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.53
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs2809115; hg19: chr14-98406425;