rs10753578

Variant names:

• chr1-162552026-G-A
• rs10753578
• ENST00000809015.1:n.287+8449C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-162552026-G-A
• chr1-162552026-G-T

Variant summary

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

The ENST00000809015.1(UAP1-DT):​n.287+8449C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,582 control chromosomes in the GnomAD database, including 4,367 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 0.23 (4367 hom., cov: 30)
• Consequence: UAP1-DT ENST00000809015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.744
• Publications: 6 publications found

Genes affected

UAP1-DT (HGNC:55410): (UAP1 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 (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809015.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UAP1-DT	ENST00000809015.1		n.287+8449C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35424 AN: 151488 Hom.: 4357 Cov.: 30

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.234 AC: 35472 AN: 151582 Hom.: 4367 Cov.: 30 AF XY: 0.237 AC XY: 17570 AN XY: 74046

African (AFR) AF: 0.218 AC: 8995 AN: 41250

American (AMR) AF: 0.293 AC: 4460 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3464

East Asian (EAS) AF: 0.312 AC: 1609 AN: 5162

South Asian (SAS) AF: 0.281 AC: 1355 AN: 4814

European-Finnish (FIN) AF: 0.227 AC: 2376 AN: 10458

Middle Eastern (MID) AF: 0.372 AC: 107 AN: 288

European-Non Finnish (NFE) AF: 0.216 AC: 14660 AN: 67908

Other (OTH) AF: 0.264 AC: 554 AN: 2102

Alfa AF: 0.229 Hom.: 5343

Bravo AF: 0.239

Asia WGS AF: 0.281 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.053
DANN	Benign	0.50
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10753578; hg19: chr1-162521816;