rs13272623

Positions:

• chr8-70632513-T-G

Variant summary

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

The ENST00000519358.5(LACTB2-AS1):​n.507T>G variant causes a non coding transcript exon 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-AS1 ENST00000519358.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

Genes affected

LACTB2-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LACTB2-AS1	NR_038881.1	n.258-19300T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LACTB2-AS1	ENST00000499227.6	n.258-19300T>G		intron_variant		1
LACTB2-AS1	ENST00000519358.5	n.507T>G		non_coding_transcript_exon_variant	3/3	2
LACTB2-AS1	ENST00000518152.1	n.338+1223T>G		intron_variant		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

Gnomad4 NFE exome AF: 0.500

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

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.0143

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.0949

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.204

Alfa AF: 0.200 Hom.: 700

Bravo AF: 0.231

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.2
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13272623; hg19: chr8-71544748;