chrY-3019783-A-C

Position:

• chrY-3019783-A-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_046502.1(LINC00278):​n.222+16566A>C variant causes a intron, non coding transcript 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 NR_046502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00278	NR_046502.1	n.222+16566A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00278	ENST00000665487.1	n.331+16566A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 20768 AN: 31564 Hom.: 0 Cov.: 0 AF XY: 0.658 AC XY: 20768 AN XY: 31564 FAILED QC

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

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.985

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.615

Alfa AF: 0.478 Hom.: 8586

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9786184; hg19: chrY-2887824;