chr1-218933208-G-A

Variant names:

• chr1-218933208-G-A
• rs10746381
• ENST00000811048.1:n.579-36108C>T

Variant summary

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

The ENST00000811048.1(LYPLAL1-DT):​n.579-36108C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,144 control chromosomes in the GnomAD database, including 52,921 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 0.80 (52921 hom., cov: 32)
• Consequence: LYPLAL1-DT ENST00000811048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.240
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811048.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LYPLAL1-DT	ENST00000811048.1		n.579-36108C>T		intron	N/A
	LYPLAL1-DT	ENST00000811049.1		n.668-1110C>T		intron	N/A
	LYPLAL1-DT	ENST00000811050.1		n.576-1110C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122360 AN: 152026 Hom.: 52897 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.981

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.932

Gnomad OTH AF: 0.862

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

GnomAD4 genome AF: 0.805 AC: 122431 AN: 152144 Hom.: 52921 Cov.: 32 AF XY: 0.812 AC XY: 60399 AN XY: 74394

African (AFR) AF: 0.456 AC: 18908 AN: 41444

American (AMR) AF: 0.910 AC: 13905 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3142 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5168 AN: 5172

South Asian (SAS) AF: 0.981 AC: 4732 AN: 4824

European-Finnish (FIN) AF: 0.969 AC: 10284 AN: 10616

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.932 AC: 63367 AN: 68016

Other (OTH) AF: 0.864 AC: 1828 AN: 2116

Alfa AF: 0.909 Hom.: 84632

Bravo AF: 0.785

Asia WGS AF: 0.954 AC: 3316 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.29
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs10746381; hg19: chr1-219106550;