rs441890

Positions:

• chr8-70652432-T-C

Variant summary

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

The NM_016027.3(LACTB2):​c.413+5324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,100 control chromosomes in the GnomAD database, including 19,690 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 0.50 (19690 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LACTB2 NM_016027.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

LACTB2 (HGNC:18512): (lactamase beta 2) Enables endoribonuclease activity; single-stranded RNA binding activity; and zinc ion binding activity. Involved in RNA phosphodiester bond hydrolysis, endonucleolytic. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]

LACTB2-AS1 (HGNC:27841): (LACTB2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.68 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LACTB2	NM_016027.3	c.413+5324A>G		intron_variant		ENST00000276590.5
LACTB2-AS1	NR_038881.1	n.340-79T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LACTB2	ENST00000276590.5	c.413+5324A>G		intron_variant		1	NM_016027.3	P1
LACTB2-AS1	ENST00000499227.6	n.340-79T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75436 AN: 151982 Hom.: 19656 Cov.: 33

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.496 AC: 75506 AN: 152100 Hom.: 19690 Cov.: 33 AF XY: 0.498 AC XY: 37059 AN XY: 74346

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.507

Gnomad4 EAS AF: 0.672

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.481

Alfa AF: 0.434 Hom.: 20163

Bravo AF: 0.494

Asia WGS AF: 0.657 AC: 2283 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
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: rs441890; hg19: chr8-71564667;