X-98609356-T-C

Variant names:

• chrX-98609356-T-C
• rs4827947
• ENST00000626665.3:n.163+30282T>C

Variant summary

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

The ENST00000626665.3(LINC03077):​n.163+30282T>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 0.81 (26037 hom., 25576 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: LINC03077 ENST00000626665.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LINC03077 (HGNC:56657): (long intergenic non-protein coding RNA 3077)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC03077	NR_186574.1	n.149+30282T>C		intron_variant	Intron 2 of 3
LINC03077	NR_186575.1	n.61-35172T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC03077	ENST00000626665.3	n.163+30282T>C		intron_variant	Intron 2 of 5	3
LINC03077	ENST00000627700.2	n.147+30282T>C		intron_variant	Intron 2 of 3	3
LINC03077	ENST00000649508.1	n.31-35172T>C		intron_variant	Intron 1 of 6
LINC03077	ENST00000650384.1	n.124-35172T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.811 AC: 88665 AN: 109345 Hom.: 26041 Cov.: 22 AF XY: 0.803 AC XY: 25515 AN XY: 31777

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.836

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.795

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: 0.811 AC: 88716 AN: 109396 Hom.: 26037 Cov.: 22 AF XY: 0.803 AC XY: 25576 AN XY: 31838

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.643

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.794

Alfa AF: 0.768 Hom.: 41764

Bravo AF: 0.816

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4827947; hg19: chrX-97864354;