6-160489867-C-T

Position:

• chr6-160489867-C-T

Variant summary

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

The NR_028092.1(LPAL2):​n.509-2435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,990 control chromosomes in the GnomAD database, including 2,453 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 0.16 (2453 hom., cov: 32)
• Consequence: LPAL2 NR_028092.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

LPAL2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPAL2	NR_028092.1	n.509-2435G>A		intron_variant
LPAL2	NR_028093.1	n.509-2435G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPAL2	ENST00000335388.5	n.509-2435G>A		intron_variant		1
LPAL2	ENST00000435757.6	n.509-2435G>A		intron_variant		1
LPAL2	ENST00000454031.6	n.549+1496G>A		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.165 AC: 24995 AN: 151870 Hom.: 2451 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.165 AC: 25007 AN: 151990 Hom.: 2453 Cov.: 32 AF XY: 0.167 AC XY: 12389 AN XY: 74268

Gnomad4 AFR AF: 0.0740

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.191

Gnomad4 OTH AF: 0.171

Alfa AF: 0.187 Hom.: 5036

Bravo AF: 0.158

Asia WGS AF: 0.320 AC: 1112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.029
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10945673; hg19: chr6-160910899;