rs12214416

Positions:

• chr6-160489485-T-A

Variant summary

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

The ENST00000335388.5(LPAL2):​n.509-2053A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0393 in 152,280 control chromosomes in the GnomAD database, including 158 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 0.039 (158 hom., cov: 33)
• Consequence: LPAL2 ENST00000335388.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

LPAL2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LPAL2	NR_028092.1	n.509-2053A>T		intron_variant
LPAL2	NR_028093.1	n.509-2053A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPAL2	ENST00000335388.5	n.509-2053A>T		intron_variant		1
LPAL2	ENST00000435757.6	n.509-2053A>T		intron_variant		1
LPAL2	ENST00000454031.6	n.549+1878A>T		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.0393 AC: 5985 AN: 152162 Hom.: 158 Cov.: 33

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0710

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0319

Gnomad SAS AF: 0.0474

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0469

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0393 AC: 5982 AN: 152280 Hom.: 158 Cov.: 33 AF XY: 0.0409 AC XY: 3044 AN XY: 74460

Gnomad4 AFR AF: 0.0101

Gnomad4 AMR AF: 0.0710

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.0476

Gnomad4 FIN AF: 0.0518

Gnomad4 NFE AF: 0.0469

Gnomad4 OTH AF: 0.0488

Alfa AF: 0.0408 Hom.: 17

Bravo AF: 0.0391

Asia WGS AF: 0.0460 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12214416; hg19: chr6-160910517;