chrX-102805306-A-C

Variant names:

• chrX-102805306-A-C
• rs17342441
• ENST00000416381.2:n.205-11686A>C

Variant summary

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

The ENST00000416381.2(LINC00630):​n.205-11686A>C variant causes a intron change. The variant allele was found at a frequency of 0.078 in 110,786 control chromosomes in the GnomAD database, including 315 homozygotes. There are 2,572 hemizygotes 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: 𝑓 0.078 (315 hom., 2572 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: LINC00630 ENST00000416381.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.97
• Publications: 1 publications found

Genes affected

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

MTND5P26 (HGNC:42295): (MT-ND5 pseudogene 26)

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=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTND5P26		n.102805306A>C		intragenic_variant
LINC00630	NR_038988.2	n.259-11686A>C		intron_variant	Intron 2 of 7
ARMCX5-GPRASP2	NR_146584.3	n.1219-20687A>C		intron_variant	Intron 8 of 18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00630	ENST00000416381.2	n.205-11686A>C		intron_variant	Intron 2 of 6	1
LINC00630	ENST00000440496.5	n.233-11686A>C		intron_variant	Intron 2 of 7	1
MTND5P26	ENST00000426018.1	n.920A>C		non_coding_transcript_exon_variant	Exon 2 of 2	6

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 8634 AN: 110737 Hom.: 315 Cov.: 22

Gnomad AFR AF: 0.0515

Gnomad AMI AF: 0.0146

Gnomad AMR AF: 0.0468

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0798

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0734

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0780 AC: 8636 AN: 110786 Hom.: 315 Cov.: 22 AF XY: 0.0773 AC XY: 2572 AN XY: 33266

African (AFR) AF: 0.0515 AC: 1583 AN: 30727

American (AMR) AF: 0.0467 AC: 486 AN: 10408

Ashkenazi Jewish (ASJ) AF: 0.0652 AC: 171 AN: 2624

East Asian (EAS) AF: 0.211 AC: 741 AN: 3516

South Asian (SAS) AF: 0.133 AC: 355 AN: 2671

European-Finnish (FIN) AF: 0.132 AC: 788 AN: 5964

Middle Eastern (MID) AF: 0.0737 AC: 16 AN: 217

European-Non Finnish (NFE) AF: 0.0834 AC: 4374 AN: 52457

Other (OTH) AF: 0.0738 AC: 112 AN: 1517

Alfa AF: 0.0806 Hom.: 612

Bravo AF: 0.0692

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	4.6
DANN	Benign	0.66
PhyloP100		6.0

Splicing

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

Other links and lift over

dbSNP: rs17342441; hg19: chrX-102060234;