X-140784294-CGTCTTCCAACAAAGGTAT-C

Position:

• chrX-140784294-CGTCTTCCAACAAAGGTAT-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NR_173139.1(LINC00632):​n.1482_1499delTGTCTTCCAACAAAGGTA 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 0.000451 in 108,656 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 5 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00045 (0 hom., 5 hem., cov: 23)
  • Exomes 𝑓: 0.0018 (0 hom. 50 hem.)
  • Failed GnomAD Quality Control
• Consequence: LINC00632 NR_173139.1 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.27

Genes affected

LINC00632 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant X-140784294-CGTCTTCCAACAAAGGTAT-C is Benign according to our data. Variant chrX-140784294-CGTCTTCCAACAAAGGTAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 2661545.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Hemizygotes in GnomAd4 at 5 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00632	NR_173139.1	n.1482_1499delTGTCTTCCAACAAAGGTA		non_coding_transcript_exon_variant	5/5
LINC00632	NR_173140.1	n.1589_1606delTGTCTTCCAACAAAGGTA		non_coding_transcript_exon_variant	5/5
LINC00632	NR_173141.1	n.1225_1242delTGTCTTCCAACAAAGGTA		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00632	ENST00000625883.2	n.1225_1242delTGTCTTCCAACAAAGGTA		non_coding_transcript_exon_variant	2/2	6
LINC00632	ENST00000648200.2	n.12331_12348delTGTCTTCCAACAAAGGTA		non_coding_transcript_exon_variant	5/5
LINC00632	ENST00000649329.1	n.1581_1598delTGTCTTCCAACAAAGGTA		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.000451 AC: 49 AN: 108603 Hom.: 0 Cov.: 23 AF XY: 0.000151 AC XY: 5 AN XY: 33007

Gnomad AFR AF: 0.00142

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000963

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000383

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00217 AC: 394 AN: 181893 Hom.: 0 AF XY: 0.000193 AC XY: 13 AN XY: 67343

Gnomad AFR exome AF: 0.00403

Gnomad AMR exome AF: 0.00209

Gnomad ASJ exome AF: 0.00391

Gnomad EAS exome AF: 0.000289

Gnomad SAS exome AF: 0.00244

Gnomad FIN exome AF: 0.00144

Gnomad NFE exome AF: 0.00212

Gnomad OTH exome AF: 0.00267

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00181 AC: 1977 AN: 1091736 Hom.: 0 AF XY: 0.000138 AC XY: 50 AN XY: 361544

Gnomad4 AFR exome AF: 0.00533

Gnomad4 AMR exome AF: 0.00160

Gnomad4 ASJ exome AF: 0.00208

Gnomad4 EAS exome AF: 0.0000994

Gnomad4 SAS exome AF: 0.00162

Gnomad4 FIN exome AF: 0.000346

Gnomad4 NFE exome AF: 0.00188

Gnomad4 OTH exome AF: 0.00147

GnomAD4 genome AF: 0.000451 AC: 49 AN: 108656 Hom.: 0 Cov.: 23 AF XY: 0.000151 AC XY: 5 AN XY: 33070

Gnomad4 AFR AF: 0.00141

Gnomad4 AMR AF: 0.0000962

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000384

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000306 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

CDR1: BS2; LINC00632: BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs760219759; hg19: chrX-139866459;