Variant 6-5144506-G-A 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_020408.6(LYRM4):c.208-35015C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0357 in 151,638 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.036 ( 114 hom., cov: 28)

Consequence

LYRM4
NM_020408.6 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.377

Variant links:

Genes affected

LYRM4 (HGNC:21365): (LYR motif containing 4) The protein encoded by this gene is found in both mitochondria and the nucleus, where it binds cysteine desulfurase and helps free inorganic sulfur for Fe/S clusters. Disruption of this gene negatively impacts mitochondrial and cytosolic iron homeostasis. [provided by RefSeq, Sep 2016]

LYRM4 links:

LYRM4-AS1 (HGNC:52055): (LYRM4 antisense RNA 1)

LYRM4-AS1 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=-0.91).

BP6

Variant 6-5144506-G-A is Benign according to our data. Variant chr6-5144506-G-A is described in ClinVar as [Benign]. Clinvar id is 1258096.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LYRM4	NM_020408.6 link	c.208-35015C>T		intron_variant		ENST00000330636.9	NP_065141.3	Q9HD34

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LYRM4	ENST00000330636.9 link	c.208-35015C>T		intron_variant		1	NM_020408.6	ENSP00000418787.1		Q9HD34

Frequencies

GnomAD3 genomes

AF:

0.0357

AC:

5405

AN:

151522

Hom.:

114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0629

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0245

Gnomad ASJ

AF:

0.100

Gnomad EAS

AF:

0.000194

Gnomad SAS

AF:

0.0125

Gnomad FIN

AF:

0.00666

Gnomad MID

AF:

0.0828

Gnomad NFE

AF:

0.0274

Gnomad OTH

AF:

0.0346

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

GnomAD4 genome

AF:

0.0357

AC:

5409

AN:

151638

Hom.:

114

Cov.:

AF XY:

0.0338

AC XY:

2505

AN XY:

74094

show subpopulations

Gnomad4 AFR

AF:

0.0628

Gnomad4 AMR

AF:

0.0245

Gnomad4 ASJ

AF:

0.100

Gnomad4 EAS

AF:

0.000195

Gnomad4 SAS

AF:

0.0127

Gnomad4 FIN

AF:

0.00666

Gnomad4 NFE

AF:

0.0274

Gnomad4 OTH

AF:

0.0343

Alfa

AF:

0.0329

Hom.:

Bravo

AF:

0.0391

Asia WGS

AF:

0.00866

AC:

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 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.68

DANN

Benign

0.52

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