Y-3019783-A-G

Variant names:

• chrY-3019783-A-G
• rs9786184
• ENST00000425031.2:n.312+16566A>G

Variant summary

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

The ENST00000425031.2(LINC00278):​n.312+16566A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: 𝑓 0.000032 (0 hom., 1 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: LINC00278 ENST00000425031.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 15 publications found

Genes affected

LINC00278 (HGNC:38712): (long intergenic non-protein coding RNA 278)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000425031.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00278	NR_046502.1		n.222+16566A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00278	ENST00000425031.2	TSL:2	n.312+16566A>G		intron	N/A
	LINC00278	ENST00000444263.6	TSL:3	n.324+16566A>G		intron	N/A
	LINC00278	ENST00000651090.1		n.324+16566A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0000317 AC: 1 AN: 31570 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000747

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000317 AC: 1 AN: 31570 Hom.: 0 Cov.: 0 AF XY: 0.0000317 AC XY: 1 AN XY: 31570

African (AFR) AF: 0.00 AC: 0 AN: 7925

American (AMR) AF: 0.00 AC: 0 AN: 3470

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 759

East Asian (EAS) AF: 0.00 AC: 0 AN: 1208

South Asian (SAS) AF: 0.000747 AC: 1 AN: 1339

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 3060

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 74

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 13094

Other (OTH) AF: 0.00 AC: 0 AN: 432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
DANN	Benign	0.12
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs9786184; hg19: chrY-2887824;