1-162535142-C-A

Variant names:

• chr1-162535142-C-A
• rs6694863
• ENST00000809015.1:n.288-3778G>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.288-3778G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0405 in 152,200 control chromosomes in the GnomAD database, including 175 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 0.041 (175 hom., cov: 33)
• Consequence: UAP1-DT ENST00000809015.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0511 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
UAP1-DT	ENST00000809015.1	n.288-3778G>T		intron_variant	Intron 2 of 3
UAP1-DT	ENST00000809016.1	n.695-3778G>T		intron_variant	Intron 2 of 3
UAP1-DT	ENST00000809017.1	n.463-3778G>T		intron_variant	Intron 1 of 2
UAP1-DT	ENST00000809018.1	n.120-3778G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0406 AC: 6168 AN: 152082 Hom.: 175 Cov.: 33

Gnomad AFR AF: 0.0177

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0497

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0593

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0511

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0405 AC: 6166 AN: 152200 Hom.: 175 Cov.: 33 AF XY: 0.0403 AC XY: 2998 AN XY: 74384

African (AFR) AF: 0.0177 AC: 737 AN: 41544

American (AMR) AF: 0.0541 AC: 827 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0497 AC: 172 AN: 3464

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5190

South Asian (SAS) AF: 0.0241 AC: 116 AN: 4816

European-Finnish (FIN) AF: 0.0593 AC: 627 AN: 10580

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0511 AC: 3474 AN: 68014

Other (OTH) AF: 0.0479 AC: 101 AN: 2110

Alfa AF: 0.0391 Hom.: 45

Bravo AF: 0.0395

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.69
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs6694863; hg19: chr1-162504932;