chr5-35952038-C-T

Variant names:

• chr5-35952038-C-T
• rs1993879
• NM_152404.4:c.*2164G>A

Variant summary

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

The NM_152404.4(UGT3A1):​c.*2164G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 151,988 control chromosomes in the GnomAD database, including 4,046 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 0.21 (4046 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UGT3A1 NM_152404.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471

Genes affected

UGT3A1 (HGNC:26625): (UDP glycosyltransferase family 3 member A1) Enables glucuronosyltransferase activity. Part of UDP-N-acetylglucosamine transferase complex. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT3A1	NM_152404.4	c.*2164G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000274278.8	NP_689617.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT3A1	ENST00000274278.8	c.*2164G>A		3_prime_UTR_variant	Exon 7 of 7	1	NM_152404.4	ENSP00000274278.3

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32109 AN: 151868 Hom.: 4049 Cov.: 32

Gnomad AFR AF: 0.0741

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.208

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.211 AC: 32105 AN: 151988 Hom.: 4046 Cov.: 32 AF XY: 0.213 AC XY: 15835 AN XY: 74266

African (AFR) AF: 0.0739 AC: 3063 AN: 41446

American (AMR) AF: 0.212 AC: 3241 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 950 AN: 3470

East Asian (EAS) AF: 0.0854 AC: 442 AN: 5176

South Asian (SAS) AF: 0.231 AC: 1109 AN: 4810

European-Finnish (FIN) AF: 0.342 AC: 3599 AN: 10516

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18835 AN: 67966

Other (OTH) AF: 0.210 AC: 444 AN: 2114

Alfa AF: 0.243 Hom.: 2509

Bravo AF: 0.195

Asia WGS AF: 0.187 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		-0.47
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

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Other links and lift over

dbSNP: rs1993879; hg19: chr5-35952140;