X-140783796-A-T

Variant names:

• chrX-140783796-A-T
• rs200866908
• ENST00000649329.2:n.1073A>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NR_173139.1(LINC00632):​n.966A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000913 in 1,095,478 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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: not found (cov: 24)
  • Exomes 𝑓: 9.1e-7 (0 hom. 0 hem.)
• Consequence: LINC00632 NR_173139.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82
• Publications: 0 publications found

Genes affected

LINC00632 (HGNC:27865): (long intergenic non-protein coding RNA 632)

CDR1 (HGNC:1798): (cerebellar degeneration related 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.10379946).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_173139.1. 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
	LINC00632	NR_173140.2	MANE Select	n.1073A>T		non_coding_transcript_exon	Exon 5 of 5
	LINC00632	NR_173139.1		n.966A>T		non_coding_transcript_exon	Exon 5 of 5
	LINC00632	NR_173141.1		n.709A>T		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00632	ENST00000649329.2	MANE Select	n.1073A>T		non_coding_transcript_exon	Exon 5 of 5
	LINC00632	ENST00000625883.2	TSL:6	n.709A>T		non_coding_transcript_exon	Exon 2 of 2
	LINC00632	ENST00000648200.2		n.11815A>T		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome AF: 9.13e-7 AC: 1 AN: 1095478 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 361934

African (AFR) AF: 0.00 AC: 0 AN: 26328

American (AMR) AF: 0.00 AC: 0 AN: 34977

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19261

East Asian (EAS) AF: 0.00 AC: 0 AN: 30194

South Asian (SAS) AF: 0.00 AC: 0 AN: 53552

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40477

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4119

European-Non Finnish (NFE) AF: 0.00000119 AC: 1 AN: 840598

Other (OTH) AF: 0.00 AC: 0 AN: 45972

GnomAD4 genome Cov.: 24

Alfa AF: 0.00 Hom.: 2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.12
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	0.46
DANN	Benign	0.22
DEOGEN2	Benign	0.033	T
FATHMM_MKL	Benign	0.025	N
LIST_S2	Benign	0.21	T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PhyloP100		-3.8
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-1.4	N
REVEL	Benign	0.049
Sift	Benign	0.20	T
Sift4G	Pathogenic	0.0	D
Polyphen		0.0010	B
Vest4		0.11
MutPred		0.69		Gain of sheet (P = 0.0221)
MVP		0.37
MPC		0.44
ClinPred		0.17	T
GERP RS		-1.1
Varity_R		0.13
gMVP		0.027
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs200866908; hg19: chrX-139865961;