rs10521499

Positions:

• chrX-102807671-C-G

Variant summary

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

The ENST00000427945.2(MTCYBP32):​n.931C>G variant causes a non coding transcript exon 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: MTCYBP32 ENST00000427945.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

Genes affected

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

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=-0.85).
• BA1: GnomAdExome4 highest population allele frequency = 1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARMCX5-GPRASP2	NR_146584.3	n.1219-18322C>G		intron_variant, non_coding_transcript_variant
LINC00630	NR_146589.1	n.190-19298C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MTCYBP32	ENST00000427945.2	n.931C>G		non_coding_transcript_exon_variant	1/1
LINC00630	ENST00000440496.5	n.233-9321C>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.598 AC: 65354 AN: 109234 Hom.: 15489 Cov.: 22 AF XY: 0.596 AC XY: 18955 AN XY: 31820

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

Gnomad4 FIN exome AF: 1.00

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

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.625

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521499; hg19: chrX-102062599;