rs13272623

Variant names:

• chr8-70632513-T-G
• rs13272623
• ENST00000499227.6:n.258-19300T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000879329.1(LACTB2):​c.*46-1316A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,216 control chromosomes in the GnomAD database, including 4,553 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 0.22 (4553 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LACTB2 ENST00000879329.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 1 publications found

Genes affected

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

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000879329.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LACTB2-AS1	NR_038881.1		n.258-19300T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LACTB2-AS1	ENST00000499227.6	TSL:1	n.258-19300T>G		intron	N/A
	LACTB2	ENST00000879329.1		c.*46-1316A>C		intron	N/A	ENSP00000549388.1
	LACTB2-AS1	ENST00000519358.6	TSL:2	n.527T>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33713 AN: 152094 Hom.: 4548 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.0140

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0949

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 2 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.222 AC: 33754 AN: 152212 Hom.: 4553 Cov.: 31 AF XY: 0.214 AC XY: 15935 AN XY: 74428

African (AFR) AF: 0.377 AC: 15627 AN: 41500

American (AMR) AF: 0.177 AC: 2701 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1087 AN: 3470

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5190

South Asian (SAS) AF: 0.138 AC: 667 AN: 4822

European-Finnish (FIN) AF: 0.0949 AC: 1007 AN: 10614

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11965 AN: 68012

Other (OTH) AF: 0.204 AC: 431 AN: 2112

Alfa AF: 0.198 Hom.: 5790

Bravo AF: 0.231

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.2
DANN	Benign	0.54
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13272623; hg19: chr8-71544748;