X-140784042-G-A

Variant names:

• chrX-140784042-G-A
• rs1326497568
• ENST00000649329.2:n.1319G>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_173139.1(LINC00632):​n.1212G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 0.0000090 (0 hom., 1 hem., cov: 24)
  • Failed GnomAD Quality Control
• Consequence: LINC00632 NR_173139.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -11.3
• Publications: 2 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.020560682).

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.1319G>A		non_coding_transcript_exon	Exon 5 of 5
	LINC00632	NR_173139.1		n.1212G>A		non_coding_transcript_exon	Exon 5 of 5
	LINC00632	NR_173141.1		n.955G>A		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.1319G>A		non_coding_transcript_exon	Exon 5 of 5
	LINC00632	ENST00000625883.2	TSL:6	n.955G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC00632	ENST00000648200.2		n.12061G>A		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.00000901 AC: 1 AN: 110962 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.0000328

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000901 AC: 1 AN: 110962 Hom.: 0 Cov.: 24 AF XY: 0.0000300 AC XY: 1 AN XY: 33292

African (AFR) AF: 0.0000328 AC: 1 AN: 30501

American (AMR) AF: 0.00 AC: 0 AN: 10414

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2637

East Asian (EAS) AF: 0.00 AC: 0 AN: 3496

South Asian (SAS) AF: 0.00 AC: 0 AN: 2586

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5975

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 233

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 52931

Other (OTH) AF: 0.00 AC: 0 AN: 1503

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.097
BayesDel_addAF	Benign	-0.49	T
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.010
DANN	Benign	0.22
DEOGEN2	Benign	0.0033	T
FATHMM_MKL	Benign	0.0055	N
LIST_S2	Benign	0.35	T
M_CAP	Benign	0.0059	T
MetaRNN	Benign	0.021	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		-11
PrimateAI	Benign	0.18	T
PROVEAN	Benign	0.53	N
REVEL	Benign	0.014
Sift	Benign	0.80	T
Sift4G	Uncertain	0.051	T
Polyphen		0.0020	B
Vest4		0.074
MutPred		0.29		Gain of phosphorylation at P109 (P = 0.0184)
MVP		0.15
MPC		0.25
ClinPred		0.031	T
GERP RS		-8.4
PromoterAI		0.0012	Neutral
Varity_R		0.019
gMVP		0.0098
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1326497568; hg19: chrX-139866207;