4-69418955-A-T

Position:

• chr4-69418955-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000514441.2(UGT2B24P):​n.1109A>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.108 in 1,608,262 control chromosomes in the GnomAD database, including 8,937 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 0.15 (2111 hom., cov: 32)
  • Exomes 𝑓: 0.10 (6826 hom.)
• Consequence: UGT2B24P ENST00000514441.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.35

Genes affected

UGT2B24P (HGNC:12548): (UDP glucuronosyltransferase family 2 member B24, pseudogene)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UGT2B24P	ENST00000514441.2	n.1109A>T		non_coding_transcript_exon_variant	5/6

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23171 AN: 151764 Hom.: 2112 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.0449

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0971

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.103 AC: 150536 AN: 1456380 Hom.: 6826 Cov.: 31 AF XY: 0.104 AC XY: 75552 AN XY: 724798

Gnomad4 AFR exome AF: 0.236

Gnomad4 AMR exome AF: 0.179

Gnomad4 ASJ exome AF: 0.115

Gnomad4 EAS exome AF: 0.0629

Gnomad4 SAS exome AF: 0.158

Gnomad4 FIN exome AF: 0.216

Gnomad4 NFE exome AF: 0.0875

Gnomad4 OTH exome AF: 0.109

GnomAD4 genome AF: 0.153 AC: 23200 AN: 151882 Hom.: 2111 Cov.: 32 AF XY: 0.158 AC XY: 11738 AN XY: 74238

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.0448

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.0972

Gnomad4 OTH AF: 0.145

Alfa AF: 0.134 Hom.: 183

Bravo AF: 0.152

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	14
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11936018; hg19: chr4-70284673;