chr1-155225189-T-C

Variant names:

• chr1-155225189-T-C
• rs2049805
• ENST00000368374.5:n.42-102A>G

Variant summary

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

The ENST00000368374.5(GBA1LP):​n.42-102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 224,830 control chromosomes in the GnomAD database, including 37,909 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 (25025 hom., cov: 33)
  • Exomes 𝑓: 0.58 (12884 hom.)
• Consequence: GBA1LP ENST00000368374.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580
• Publications: 70 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000368374.5. 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.153+2193A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GBA1LP	ENST00000368374.5	TSL:1	n.42-102A>G		intron	N/A
	GBA1LP	ENST00000459805.6	TSL:5	n.83-102A>G		intron	N/A
	GBA1LP	ENST00000463838.7	TSL:2	n.158+2193A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86341 AN: 151876 Hom.: 24986 Cov.: 33

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.557

GnomAD4 exome AF: 0.583 AC: 42485 AN: 72836 Hom.: 12884 AF XY: 0.582 AC XY: 23431 AN XY: 40236

African (AFR) AF: 0.701 AC: 2618 AN: 3734

American (AMR) AF: 0.665 AC: 3958 AN: 5952

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 799 AN: 1618

East Asian (EAS) AF: 0.790 AC: 4847 AN: 6132

South Asian (SAS) AF: 0.570 AC: 7632 AN: 13382

European-Finnish (FIN) AF: 0.582 AC: 1381 AN: 2372

Middle Eastern (MID) AF: 0.447 AC: 93 AN: 208

European-Non Finnish (NFE) AF: 0.533 AC: 19325 AN: 36248

Other (OTH) AF: 0.574 AC: 1832 AN: 3190

GnomAD4 genome AF: 0.569 AC: 86427 AN: 151994 Hom.: 25025 Cov.: 33 AF XY: 0.570 AC XY: 42368 AN XY: 74286

African (AFR) AF: 0.654 AC: 27071 AN: 41422

American (AMR) AF: 0.613 AC: 9359 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3468

East Asian (EAS) AF: 0.777 AC: 4027 AN: 5182

South Asian (SAS) AF: 0.538 AC: 2592 AN: 4820

European-Finnish (FIN) AF: 0.548 AC: 5779 AN: 10552

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

European-Non Finnish (NFE) AF: 0.505 AC: 34298 AN: 67980

Other (OTH) AF: 0.552 AC: 1165 AN: 2110

Alfa AF: 0.527 Hom.: 92950

Bravo AF: 0.583

Asia WGS AF: 0.669 AC: 2328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.77
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs2049805; hg19: chr1-155194980;