1-155227671-C-T

Variant names:

• chr1-155227671-C-T
• rs2990245
• ENST00000687347.2:n.17G>A

Variant summary

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

The ENST00000687347.2(GBA1LP):​n.17G>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 0.566 in 152,094 control chromosomes in the GnomAD database, including 24,811 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 0.57 (24811 hom., cov: 34)
• Consequence: GBA1LP ENST00000687347.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394
• Publications: 37 publications found

Genes affected

GBA1LP (HGNC:):

GBA1LP (HGNC:4178): (glucosylceramidase beta 1 like, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687347.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GBA1LP	NR_002188.3		n.-137G>A		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GBA1LP	ENST00000687347.2		n.17G>A		non_coding_transcript_exon	Exon 1 of 1
	GBA1LP	ENST00000790258.1		n.117+240G>A		intron	N/A
	GBA1LP	ENST00000368374.5	TSL:1	n.-249G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86031 AN: 151976 Hom.: 24785 Cov.: 34

Gnomad AFR AF: 0.651

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.566 AC: 86098 AN: 152094 Hom.: 24811 Cov.: 34 AF XY: 0.568 AC XY: 42240 AN XY: 74382

African (AFR) AF: 0.651 AC: 26999 AN: 41472

American (AMR) AF: 0.610 AC: 9327 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3472

East Asian (EAS) AF: 0.778 AC: 4031 AN: 5184

South Asian (SAS) AF: 0.538 AC: 2600 AN: 4830

European-Finnish (FIN) AF: 0.548 AC: 5802 AN: 10588

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34021 AN: 67954

Other (OTH) AF: 0.549 AC: 1158 AN: 2110

Alfa AF: 0.518 Hom.: 11149

Bravo AF: 0.580

Asia WGS AF: 0.666 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.39
DANN	Benign	0.67
PhyloP100		-0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2990245;

hg19: chr1-155197462;