6-160458599-T-C

Position:

• chr6-160458599-T-C

Variant summary

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

The variant allele was found at a frequency of 0.258 in 152,140 control chromosomes in the GnomAD database, including 5,438 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 0.26 (5438 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.160458599T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LPAL2	ENST00000454031.6	n.2222+457A>G		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39265 AN: 152022 Hom.: 5439 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.258 AC: 39276 AN: 152140 Hom.: 5438 Cov.: 32 AF XY: 0.262 AC XY: 19474 AN XY: 74386

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.294

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.297

Alfa AF: 0.271 Hom.: 702

Bravo AF: 0.249

Asia WGS AF: 0.390 AC: 1354 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	2.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1567438; hg19: chr6-160879631;