Y-3019783-A-C

Variant names:

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

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>C 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 0.66 (0 hom., 20838 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=-1.0).

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>C		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.658 AC: 20768 AN: 31564 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.984

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.986

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.609

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: InbreedingCoeff AF: 0.659 AC: 20838 AN: 31625 Hom.: 0 Cov.: 0 AF XY: 0.659 AC XY: 20838 AN XY: 31625

African (AFR) AF: 0.808 AC: 6440 AN: 7975

American (AMR) AF: 0.512 AC: 1781 AN: 3476

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 681 AN: 759

East Asian (EAS) AF: 0.999 AC: 1206 AN: 1207

South Asian (SAS) AF: 0.985 AC: 1322 AN: 1342

European-Finnish (FIN) AF: 0.975 AC: 2982 AN: 3059

Middle Eastern (MID) AF: 0.986 AC: 72 AN: 73

European-Non Finnish (NFE) AF: 0.460 AC: 6025 AN: 13091

Other (OTH) AF: 0.615 AC: 267 AN: 434

Alfa AF: 0.536 Hom.: 14936

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.13
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;