Variant chr5-131171208-TTG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_181705.4(LYRM7):c.18+173_18+174del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,846 control chromosomes in the GnomAD database, including 6,231 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.18 ( 6231 hom., cov: 30)

Consequence

LYRM7
NM_181705.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.356

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 5-131171208-TTG-T is Benign according to our data. Variant chr5-131171208-TTG-T is described in ClinVar as [Benign]. Clinvar id is 1252214.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
LYRM7	NM_181705.4 linkuse as main transcript	c.18+173_18+174del	intron_variant	ENST00000379380.9
LYRM7	NM_001293735.2 linkuse as main transcript	c.18+173_18+174del	intron_variant
LYRM7	NR_121658.2 linkuse as main transcript	n.95+173_95+174del	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
LYRM7	ENST00000379380.9 linkuse as main transcript	c.18+173_18+174del	intron_variant	1	NM_181705.4	P1
LYRM7	ENST00000507584.1 linkuse as main transcript	c.18+173_18+174del	intron_variant	2
LYRM7	ENST00000510516.5 linkuse as main transcript	c.18+173_18+174del	intron_variant	2
HINT1	ENST00000506207.2 linkuse as main transcript	n.236+396_236+397del	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27281

AN:

151728

Hom.:

6215

Cov.:

show subpopulations

Gnomad AFR

AF:

0.537

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0921

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.0484

Gnomad FIN

AF:

0.00916

Gnomad MID

AF:

0.175

Gnomad NFE

AF:

0.0391

Gnomad OTH

AF:

0.160

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.180

AC:

27334

AN:

151846

Hom.:

6231

Cov.:

AF XY:

0.174

AC XY:

12944

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.537

Gnomad4 AMR

AF:

0.0919

Gnomad4 ASJ

AF:

0.111

Gnomad4 EAS

AF:

0.000967

Gnomad4 SAS

AF:

0.0485

Gnomad4 FIN

AF:

0.00916

Gnomad4 NFE

AF:

0.0391

Gnomad4 OTH

AF:

0.158

Alfa

AF:

0.122

Hom.:

458

Bravo

AF:

0.203

Asia WGS

AF:

0.0640

AC:

225

AN:

3478

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 19, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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