chrY-8634195-A-T

Variant names:

• chrY-8634195-A-T
• rs9786140
• ENST00000650816.1:n.243-44162A>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000650816.1(LINC00279):​n.243-44162A>T variant causes a intron change. 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: 0)
• Consequence: LINC00279 ENST00000650816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 8 publications found

Genes affected

LINC00279 (HGNC:38724): (long intergenic non-protein coding RNA 279)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00279	ENST00000650816.1	n.243-44162A>T		intron_variant	Intron 1 of 11
LINC00279	ENST00000651700.2	n.196-44162A>T		intron_variant	Intron 1 of 7
LINC00279	ENST00000651793.1	n.1448+968A>T		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes Cov.: 0

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

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.25

Splicing

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

Other links and lift over

dbSNP: rs9786140; hg19: chrY-8502236;