4-69418955-A-T

Variant names:

• chr4-69418955-A-T
• rs11936018
• ENST00000514441.2:n.1109A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000514441.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UGT2B24P	ENST00000514441.2	TSL:6	n.1109A>T		non_coding_transcript_exon	Exon 5 of 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

African (AFR) AF: 0.236 AC: 7806 AN: 33102

American (AMR) AF: 0.179 AC: 7963 AN: 44592

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 2996 AN: 26018

East Asian (EAS) AF: 0.0629 AC: 2494 AN: 39676

South Asian (SAS) AF: 0.158 AC: 13591 AN: 86094

European-Finnish (FIN) AF: 0.216 AC: 11543 AN: 53382

Middle Eastern (MID) AF: 0.129 AC: 740 AN: 5736

European-Non Finnish (NFE) AF: 0.0875 AC: 96872 AN: 1107664

Other (OTH) AF: 0.109 AC: 6531 AN: 60116

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

African (AFR) AF: 0.245 AC: 10139 AN: 41444

American (AMR) AF: 0.153 AC: 2321 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 400 AN: 3466

East Asian (EAS) AF: 0.0448 AC: 230 AN: 5136

South Asian (SAS) AF: 0.163 AC: 784 AN: 4818

European-Finnish (FIN) AF: 0.215 AC: 2274 AN: 10580

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0972 AC: 6598 AN: 67908

Other (OTH) AF: 0.145 AC: 307 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	14
DANN	Benign	0.84
PhyloP100		6.3

Splicing

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

Other links and lift over

dbSNP: rs11936018; hg19: chr4-70284673;