rs11726322

Variant names:

• chr4-68825803-G-C
• rs11726322
• NM_001075.6:c.1000-607G>C

Variant summary

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

The NM_001075.6(UGT2B10):​c.1000-607G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,982 control chromosomes in the GnomAD database, including 1,947 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 (1947 hom., cov: 32)
• Consequence: UGT2B10 NM_001075.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.717
• Publications: 5 publications found

Genes affected

UGT2B10 (HGNC:12544): (UDP glucuronosyltransferase family 2 member B10) Predicted to be involved in lipid metabolic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B10	NM_001075.6	c.1000-607G>C		intron_variant	Intron 3 of 5	ENST00000265403.12	NP_001066.1
UGT2B10	NM_001144767.3	c.748-607G>C		intron_variant	Intron 3 of 5		NP_001138239.1
UGT2B10	NM_001290091.2	c.256-607G>C		intron_variant	Intron 3 of 5		NP_001277020.1
UGT2B10	XM_017008585.3	c.991-607G>C		intron_variant	Intron 3 of 5		XP_016864074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B10	ENST00000265403.12	c.1000-607G>C		intron_variant	Intron 3 of 5	1	NM_001075.6	ENSP00000265403.7
UGT2B10	ENST00000458688.2	c.748-607G>C		intron_variant	Intron 3 of 5	2		ENSP00000413420.2

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22786 AN: 151864 Hom.: 1946 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.150 AC: 22799 AN: 151982 Hom.: 1947 Cov.: 32 AF XY: 0.149 AC XY: 11028 AN XY: 74262

African (AFR) AF: 0.232 AC: 9602 AN: 41440

American (AMR) AF: 0.109 AC: 1657 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3470

East Asian (EAS) AF: 0.184 AC: 951 AN: 5162

South Asian (SAS) AF: 0.129 AC: 624 AN: 4820

European-Finnish (FIN) AF: 0.101 AC: 1069 AN: 10562

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7858 AN: 67966

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.128 Hom.: 177

Bravo AF: 0.156

Asia WGS AF: 0.138 AC: 480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.41
PhyloP100		-0.72
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

Other links and lift over

dbSNP: rs11726322; hg19: chr4-69691521;