rs6703753

Variant names:

• chr1-218990018-C-T
• rs6703753
• ENST00000657470.1:n.1893G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000657470.1(LYPLAL1-DT):​n.1893G>A variant causes a non coding transcript exon 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 ENST00000657470.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LYPLAL1-DT	ENST00000657470.1	n.1893G>A		non_coding_transcript_exon_variant	Exon 6 of 6
LYPLAL1-DT	ENST00000663684.1	n.364-6735G>A		intron_variant	Intron 4 of 4
LYPLAL1-DT	ENST00000685043.2	n.786+1253G>A		intron_variant	Intron 5 of 5

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

African (AFR) AF: 0.585 AC: 24248 AN: 41430

American (AMR) AF: 0.232 AC: 3553 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 924 AN: 3470

East Asian (EAS) AF: 0.0184 AC: 95 AN: 5160

South Asian (SAS) AF: 0.137 AC: 663 AN: 4824

European-Finnish (FIN) AF: 0.162 AC: 1707 AN: 10542

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 14989 AN: 67952

Other (OTH) AF: 0.299 AC: 632 AN: 2112

Alfa AF: 0.249 Hom.: 21763

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6703753; hg19: chr1-219163360;