6-5143955-T-C

Position:

• chr6-5143955-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The NM_020408.6(LYRM4):​c.208-34464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 152,062 control chromosomes in the GnomAD database, including 16,883 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.45 (16883 hom., cov: 33)
• Consequence: LYRM4 NM_020408.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.35

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-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BP6: Variant 6-5143955-T-C is Benign according to our data. Variant chr6-5143955-T-C is described in ClinVar as [Benign]. Clinvar id is 680628.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYRM4	NM_020408.6	c.208-34464A>G		intron_variant		ENST00000330636.9
LYRM4-AS1	NR_126015.1	n.373+71221T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYRM4	ENST00000330636.9	c.208-34464A>G		intron_variant		1	NM_020408.6	P1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67874 AN: 151944 Hom.: 16873 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.452

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

GnomAD4 genome AF: 0.447 AC: 67914 AN: 152062 Hom.: 16883 Cov.: 33 AF XY: 0.455 AC XY: 33787 AN XY: 74310

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.456

Alfa AF: 0.465 Hom.: 2154

Bravo AF: 0.429

Asia WGS AF: 0.576 AC: 2000 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	17
DANN	Benign	0.82

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

Other links and lift over

dbSNP: rs445204; hg19: chr6-5144189;