X-140783982-T-A

Position:

• chrX-140783982-T-A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_173139.1(LINC00632):​n.1152T>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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 24)
• Consequence: LINC00632 NR_173139.1 non_coding_transcript_exon
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -5.93

Genes affected

LINC00632 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.04892829).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00632	NR_173139.1	n.1152T>A		non_coding_transcript_exon_variant	5/5
LINC00632	NR_173140.1	n.1259T>A		non_coding_transcript_exon_variant	5/5
LINC00632	NR_173141.1	n.895T>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00632	ENST00000625883.2	n.895T>A		non_coding_transcript_exon_variant	2/2	6
LINC00632	ENST00000648200.2	n.12001T>A		non_coding_transcript_exon_variant	5/5
LINC00632	ENST00000648347.1	n.691T>A		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes Cov.: 24

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 24

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 03, 2023

The c.385A>T (p.S129C) alteration is located in exon 1 (coding exon 1) of the CDR1 gene. This alteration results from a A to T substitution at nucleotide position 385, causing the serine (S) at amino acid position 129 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.072
BayesDel_addAF	Benign	-0.46	T
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.90
DEOGEN2	Benign	0.021	T
FATHMM_MKL	Benign	0.0027	N
LIST_S2	Benign	0.35	T
M_CAP	Benign	0.0076	T
MetaRNN	Benign	0.049	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.34	N
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.010
Sift	Benign	0.18	T
Sift4G	Benign	0.20	T
Polyphen		0.011	B
Vest4		0.14
MutPred		0.38		Gain of catalytic residue at M127 (P = 0.0081);
MVP		0.20
MPC		0.76
ClinPred		0.50	T
GERP RS		-6.6
Varity_R		0.057
gMVP		0.0062

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-139866147;