6-5109711-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020408.6(LYRM4):c.208-220G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.938 in 152,226 control chromosomes in the GnomAD database, including 67,106 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.94 (67106 hom., cov: 32)
• Consequence: LYRM4 NM_020408.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.04

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 6-5109711-C-T is Benign according to our data. Variant chr6-5109711-C-T is described in ClinVar as [Benign]. Clinvar id is 680632.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LYRM4	NM_020408.6	c.208-220G>A		intron_variant		ENST00000330636.9
LYRM4-AS1	NR_126015.1	n.373+36977C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYRM4	ENST00000330636.9	c.208-220G>A		intron_variant		1	NM_020408.6	P1

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142672 AN: 152108 Hom.: 67041 Cov.: 32

Gnomad AFR AF: 0.985

Gnomad AMI AF: 0.985

Gnomad AMR AF: 0.869

Gnomad ASJ AF: 0.926

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.933

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.938 AC: 142796 AN: 152226 Hom.: 67106 Cov.: 32 AF XY: 0.936 AC XY: 69674 AN XY: 74408

Gnomad4 AFR AF: 0.985

Gnomad4 AMR AF: 0.869

Gnomad4 ASJ AF: 0.926

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.928

Gnomad4 OTH AF: 0.918

Alfa AF: 0.936 Hom.: 8283

Bravo AF: 0.932

Asia WGS AF: 0.941 AC: 3272 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	-0.99
Cadd	Benign	0.13
Dann	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs434706; hg19: chr6-5109945;