X-102807671-C-G

Variant names:

• chrX-102807671-C-G
• rs10521499
• ENST00000416381.2:n.205-9321C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000416381.2(LINC00630):​n.205-9321C>G 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 0.60 (15484 hom., 18968 hem., cov: 22)
  • Exomes 𝑓: 1.0 (0 hom. 1 hem.)
  • Failed GnomAD Quality Control
• Consequence: LINC00630 ENST00000416381.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 publications found

Genes affected

LINC00630 (HGNC:44263): (long intergenic non-protein coding RNA 630)

MTCYBP32 (HGNC:52174): (MT-CYB pseudogene 32)

ARMCX5-GPRASP2 (HGNC:42000): (ARMCX5-GPRASP2 readthrough) This locus represents naturally occurring readthrough transcription among the adjacent armadillo repeat containing, X-linked 5 (ARMCX5), G protein-coupled receptor associated sorting proteins 1 and 2 (GPRASP1 and GPRASP2), basic helix-loop-helix family member b9 (BHLHB9), and long intergenic non-protein coding RNA 630 (LINC00630) genes on chromosome X. Transcripts may make use of multiple alternative promoters and polyadenylation signals in this region. Readthrough transcripts may produce proteins identical to the proteins encoded by GPRASP2 or BHLHB9. [provided by RefSeq, Apr 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAdExome4 highest population allele frequency = 1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTCYBP32		n.102807671C>G		intragenic_variant
LINC00630	NR_038988.2	n.259-9321C>G		intron_variant	Intron 2 of 7
ARMCX5-GPRASP2	NR_146584.3	n.1219-18322C>G		intron_variant	Intron 8 of 18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00630	ENST00000416381.2	n.205-9321C>G		intron_variant	Intron 2 of 6	1
LINC00630	ENST00000440496.5	n.233-9321C>G		intron_variant	Intron 2 of 7	1
MTCYBP32	ENST00000427945.2	n.931C>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.598 AC: 65354 AN: 109234 Hom.: 15489 Cov.: 22

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.862

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.695

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.632

GnomAD4 exome AF: 1.00 AC: 1 AN: 1 Hom.: 0 Cov.: 0 AF XY: 1.00 AC XY: 1 AN XY: 1

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 1 AN: 1

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.598 AC: 65349 AN: 109284 Hom.: 15484 Cov.: 22 AF XY: 0.595 AC XY: 18968 AN XY: 31880

African (AFR) AF: 0.287 AC: 8706 AN: 30352

American (AMR) AF: 0.756 AC: 7711 AN: 10197

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 1939 AN: 2589

East Asian (EAS) AF: 0.558 AC: 1928 AN: 3456

South Asian (SAS) AF: 0.462 AC: 1184 AN: 2562

European-Finnish (FIN) AF: 0.667 AC: 3849 AN: 5774

Middle Eastern (MID) AF: 0.706 AC: 151 AN: 214

European-Non Finnish (NFE) AF: 0.738 AC: 38372 AN: 51986

Other (OTH) AF: 0.625 AC: 920 AN: 1471

Alfa AF: 0.657 Hom.: 5247

Bravo AF: 0.599

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.28
DANN	Benign	0.50
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10521499; hg19: chrX-102062599;