rs6703753

Positions:

• chr1-218990018-C-T

Variant summary

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

The ENST00000691001.1(LYPLAL1-DT):​n.629+1253G>A 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 0.31 in 151,976 control chromosomes in the GnomAD database, including 9,844 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 0.31 (9844 hom., cov: 32)
• Consequence: LYPLAL1-DT ENST00000691001.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299

Genes affected

LYPLAL1-DT (HGNC:50560): (LYPLAL1 divergent transcript)

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 (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LYPLAL1-DT	ENST00000691001.1	n.629+1253G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47112 AN: 151858 Hom.: 9831 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0184

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.310 AC: 47158 AN: 151976 Hom.: 9844 Cov.: 32 AF XY: 0.303 AC XY: 22476 AN XY: 74288

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0184

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.299

Alfa AF: 0.236 Hom.: 8982

Bravo AF: 0.328

Asia WGS AF: 0.109 AC: 383 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	3.9
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: rs6703753; hg19: chr1-219163360;