1-218975956-A-G

Variant names:

• chr1-218975956-A-G
• rs618171
• ENST00000811069.1:n.962T>C

Variant summary

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

The ENST00000811069.1(LYPLAL1-DT):​n.962T>C 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 0.576 in 152,074 control chromosomes in the GnomAD database, including 28,685 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 0.58 (28685 hom., cov: 32)
• Consequence: LYPLAL1-DT ENST00000811069.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 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	ENST00000811069.1	n.962T>C		non_coding_transcript_exon_variant	Exon 7 of 8
LYPLAL1-DT	ENST00000811048.1	n.579-78856T>C		intron_variant	Intron 3 of 4
LYPLAL1-DT	ENST00000811049.1	n.668-43858T>C		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87545 AN: 151956 Hom.: 28687 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.576 AC: 87560 AN: 152074 Hom.: 28685 Cov.: 32 AF XY: 0.578 AC XY: 42936 AN XY: 74342

African (AFR) AF: 0.257 AC: 10676 AN: 41464

American (AMR) AF: 0.546 AC: 8339 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2338 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2681 AN: 5156

South Asian (SAS) AF: 0.631 AC: 3042 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8651 AN: 10574

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49782 AN: 67982

Other (OTH) AF: 0.584 AC: 1234 AN: 2112

Alfa AF: 0.675 Hom.: 56977

Bravo AF: 0.544

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs618171; hg19: chr1-219149298;