X-98609356-T-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626665.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03077	NR_186574.1		n.149+30282T>C		intron	N/A
	LINC03077	NR_186575.1		n.61-35172T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC03077	ENST00000626665.3	TSL:3	n.163+30282T>C		intron	N/A
	LINC03077	ENST00000627700.2	TSL:3	n.147+30282T>C		intron	N/A
	LINC03077	ENST00000649508.1		n.31-35172T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.811 AC: 88665 AN: 109345 Hom.: 26041 Cov.: 22

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

African (AFR) AF: 0.937 AC: 28304 AN: 30204

American (AMR) AF: 0.781 AC: 7906 AN: 10121

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2177 AN: 2611

East Asian (EAS) AF: 0.643 AC: 2191 AN: 3409

South Asian (SAS) AF: 0.595 AC: 1512 AN: 2542

European-Finnish (FIN) AF: 0.828 AC: 4753 AN: 5737

Middle Eastern (MID) AF: 0.834 AC: 176 AN: 211

European-Non Finnish (NFE) AF: 0.762 AC: 39928 AN: 52402

Other (OTH) AF: 0.794 AC: 1182 AN: 1488

Alfa AF: 0.788 Hom.: 56581

Bravo AF: 0.816

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.37
DANN	Benign	0.51
PhyloP100		-1.0

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4827947;

hg19: chrX-97864354;