rs17005517

Positions:

• chr1-219431111-C-A
• chr1-219431111-C-G
• chr1-219431111-C-T

Variant summary

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

The ENST00000441790.2(LYPLAL1-AS1):​n.121-19172G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,040 control chromosomes in the GnomAD database, including 5,053 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 0.25 (5053 hom., cov: 32)
• Consequence: LYPLAL1-AS1 ENST00000441790.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.767

Genes affected

LYPLAL1-AS1 (HGNC:54054): (LYPLAL1 antisense RNA 1)

LOC107984018 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984018	XR_002958460.2	n.146+1792G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYPLAL1-AS1	ENST00000441790.2	n.121-19172G>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38699 AN: 151922 Hom.: 5051 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.465

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.255 AC: 38712 AN: 152040 Hom.: 5053 Cov.: 32 AF XY: 0.249 AC XY: 18530 AN XY: 74328

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.237

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.261

Alfa AF: 0.271 Hom.: 11265

Bravo AF: 0.255

Asia WGS AF: 0.210 AC: 730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17005517; hg19: chr1-219604453;