rs733168

chr1-54816883-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001110533.2(LEXM):c.1051-106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 1,417,278 control chromosomes in the GnomAD database, including 303,562 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.61 (28941 hom., cov: 31)
  • Exomes 𝑓: 0.66 (274621 hom.)
• Consequence: LEXM NM_001110533.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.859

Genes affected

LEXM (HGNC:):

CIMAP2 (HGNC:26854): (ciliary microtubule associated protein 2) Predicted to enable mitochondrial ribosome binding activity. Predicted to act upstream of or within positive regulation of cell population proliferation and positive regulation of oxidative phosphorylation. Predicted to be located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LEXM	NM_001110533.2	c.1051-106A>G		intron_variant		ENST00000371273.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CIMAP2	ENST00000371273.4	c.1051-106A>G		intron_variant		1	NM_001110533.2	A2
CIMAP2	ENST00000358193.7	c.1051-106A>G		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.611 AC: 92765 AN: 151834 Hom.: 28950 Cov.: 31

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.606

GnomAD4 exome AF: 0.656 AC: 830080 AN: 1265324 Hom.: 274621 AF XY: 0.658 AC XY: 411010 AN XY: 624206

Gnomad4 AFR exome AF: 0.487

Gnomad4 AMR exome AF: 0.545

Gnomad4 ASJ exome AF: 0.638

Gnomad4 EAS exome AF: 0.454

Gnomad4 SAS exome AF: 0.736

Gnomad4 FIN exome AF: 0.726

Gnomad4 NFE exome AF: 0.665

Gnomad4 OTH exome AF: 0.638

GnomAD4 genome AF: 0.611 AC: 92786 AN: 151954 Hom.: 28941 Cov.: 31 AF XY: 0.616 AC XY: 45706 AN XY: 74252

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.748

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.608

Alfa AF: 0.645 Hom.: 3974

Bravo AF: 0.582

Asia WGS AF: 0.584 AC: 2034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.19
Dann	Benign	0.40

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: rs733168; hg19: chr1-55282556; COSMIC: COSV64022882;