Variant rs10521499 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.161

Variant links:

Genes affected

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

LINC00630 links:

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

MTCYBP32 links:

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]

ARMCX5-GPRASP2 links:

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ACMG classification

Classification made for transcript

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	Effect
MTCYBP32		n.102807671C>G	intragenic_variant
LINC00630	NR_038988.2 link	n.259-9321C>G	intron_variant
ARMCX5-GPRASP2	NR_146584.3 link	n.1219-18322C>G	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LINC00630	ENST00000416381.2 link	n.205-9321C>G	intron_variant		1
LINC00630	ENST00000440496.5 link	n.233-9321C>G	intron_variant		1
MTCYBP32	ENST00000427945.2 link	n.931C>G	non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes

AF:

0.598

AC:

65354

AN:

109234

Hom.:

15489

Cov.:

AF XY:

0.596

AC XY:

18955

AN XY:

31820

show subpopulations

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:

AN:

Hom.:

Cov.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

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.:

AF XY:

0.595

AC XY:

18968

AN XY:

31880

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over