dbSNP rs17342441: LINC00630:n.205-11686A>C (chrX-102805306-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.97

Publications

1 publications found

Variant links:

Genes affected

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

LINC00630 links:

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

MTND5P26 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 was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426018.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LINC00630	NR_038988.2	n.259-11686A>C	intron	N/A
ARMCX5-GPRASP2	NR_146584.3	n.1219-20687A>C	intron	N/A
ARMCX5-GPRASP2	NR_146587.2	n.611-11686A>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC00630	ENST00000416381.2	TSL:1	n.205-11686A>C	intron	N/A
LINC00630	ENST00000440496.5	TSL:1	n.233-11686A>C	intron	N/A
MTND5P26	ENST00000426018.1	TSL:6	n.920A>C	non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0780

AC:

8634

AN:

110737

Hom.:

315

Cov.:

show subpopulations

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:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0780

AC:

8636

AN:

110786

Hom.:

315

Cov.:

AF XY:

0.0773

AC XY:

2572

AN XY:

33266

show subpopulations

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:

AN:

217

European-Non Finnish (NFE)

AF:

0.0834

AC:

4374

AN:

52457

Other (OTH)

AF:

0.0738

AC:

112

AN:

1517

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

290

580

870

1160

1450

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

200

300

400

500

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0806

Hom.:

612

Bravo

AF:

0.0692

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

4.6

(source)

DANN

Benign

0.66

PhyloP100

6.0

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over