chrX-102805306-A-C

Position:

• chrX-102805306-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426018.1(MTND5P26):​n.920A>C variant causes a non coding transcript exon 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: MTND5P26 ENST00000426018.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.97

Genes affected

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

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

ARMCX5-GPRASP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ARMCX5-GPRASP2	NR_146584.3	n.1219-20687A>C		intron_variant, non_coding_transcript_variant
LINC00630	NR_146589.1	n.190-21663A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTND5P26	ENST00000426018.1	n.920A>C		non_coding_transcript_exon_variant	2/2
LINC00630	ENST00000440496.5	n.233-11686A>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0780 AC: 8634 AN: 110737 Hom.: 315 Cov.: 22 AF XY: 0.0774 AC XY: 2570 AN XY: 33207

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

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

Gnomad4 AFR AF: 0.0515

Gnomad4 AMR AF: 0.0467

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.0834

Gnomad4 OTH AF: 0.0738

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17342441; hg19: chrX-102060234;