Variant chr5-131182077-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_181705.4(LYRM7):c.92-152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0658 in 658,528 control chromosomes in the GnomAD database, including 1,888 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.061 ( 442 hom., cov: 32)

Exomes 𝑓: 0.067 ( 1446 hom. )

Consequence

LYRM7
NM_181705.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.411

Variant links:

Genes affected

LYRM7 (HGNC:28072): (LYR motif containing 7) Inner mitochondrial membrane complex III (CIII) is the main enzyme complex in the mitochondrial respiratory chain, and Rieske Fe-S protein (UQCRFS1) is the last catalytic subunit added to the complex. The protein encoded by this gene is a nuclear-encoded mitochondrial matrix protein that stabilizes UQCRFS1 and chaperones it to the CIII complex. Defects in this gene are a cause of mitochondrial complex III deficiency, nuclear type 8. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2014]

LYRM7 links:

HINT1 (HGNC:4912): (histidine triad nucleotide binding protein 1) This gene encodes a protein that hydrolyzes purine nucleotide phosphoramidates substrates, including AMP-morpholidate, AMP-N-alanine methyl ester, AMP-alpha-acetyl lysine methyl ester, and AMP-NH2. The encoded protein interacts with these substrates via a histidine triad motif. This gene is considered a tumor suppressor gene. In addition, mutations in this gene can cause autosomal recessive neuromyotonia and axonal neuropathy. There are several related pseudogenes on chromosome 7. Several transcript variants have been observed. [provided by RefSeq, Dec 2015]

HINT1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 5-131182077-A-G is Benign according to our data. Variant chr5-131182077-A-G is described in ClinVar as [Benign]. Clinvar id is 1273649.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
LYRM7	NM_181705.4 linkuse as main transcript	c.92-152A>G	intron_variant	ENST00000379380.9
LYRM7	NM_001293735.2 linkuse as main transcript	c.92-152A>G	intron_variant
LYRM7	NR_121658.2 linkuse as main transcript	n.168+1910A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
LYRM7	ENST00000379380.9 linkuse as main transcript	c.92-152A>G	intron_variant	1	NM_181705.4	P1
LYRM7	ENST00000507584.1 linkuse as main transcript	c.92-152A>G	intron_variant	2
LYRM7	ENST00000510516.5 linkuse as main transcript	c.91+1910A>G	intron_variant	2
HINT1	ENST00000506207.2 linkuse as main transcript	n.109-10344T>C	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0613

AC:

9325

AN:

152178

Hom.:

440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0150

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.0530

Gnomad EAS

AF:

0.0452

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0815

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0654

Gnomad OTH

AF:

0.0698

GnomAD4 exome

AF:

0.0672

AC:

34008

AN:

506232

Hom.:

1446

AF XY:

0.0701

AC XY:

18165

AN XY:

259298

show subpopulations

Gnomad4 AFR exome

AF:

0.00954

Gnomad4 AMR exome

AF:

0.178

Gnomad4 ASJ exome

AF:

0.0575

Gnomad4 EAS exome

AF:

0.0252

Gnomad4 SAS exome

AF:

0.118

Gnomad4 FIN exome

AF:

0.0880

Gnomad4 NFE exome

AF:

0.0617

Gnomad4 OTH exome

AF:

0.0631

GnomAD4 genome

AF:

0.0614

AC:

9345

AN:

152296

Hom.:

442

Cov.:

AF XY:

0.0643

AC XY:

4789

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0149

Gnomad4 AMR

AF:

0.146

Gnomad4 ASJ

AF:

0.0530

Gnomad4 EAS

AF:

0.0457

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.0815

Gnomad4 NFE

AF:

0.0655

Gnomad4 OTH

AF:

0.0714

Alfa

AF:

0.0666

Hom.:

Bravo

AF:

0.0634

Asia WGS

AF:

0.104

AC:

359

AN:

3452

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.72

DANN

Benign

0.54

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over