4-68817137-T-G

Variant names:

• chr4-68817137-T-G
• rs835309
• NM_001075.6:c.718+400T>G

Variant summary

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

The NM_001075.6(UGT2B10):​c.718+400T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.783 in 151,640 control chromosomes in the GnomAD database, including 49,490 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 0.78 (49490 hom., cov: 32)
• Consequence: UGT2B10 NM_001075.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 10 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B10	NM_001075.6	c.718+400T>G		intron_variant	Intron 1 of 5	ENST00000265403.12	NP_001066.1
UGT2B10	NM_001144767.3	c.466+652T>G		intron_variant	Intron 1 of 5		NP_001138239.1
UGT2B10	NM_001290091.2	c.-26-892T>G		intron_variant	Intron 1 of 5		NP_001277020.1
UGT2B10	XM_017008585.3	c.718+400T>G		intron_variant	Intron 1 of 5		XP_016864074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B10	ENST00000265403.12	c.718+400T>G		intron_variant	Intron 1 of 5	1	NM_001075.6	ENSP00000265403.7
UGT2B10	ENST00000458688.2	c.466+652T>G		intron_variant	Intron 1 of 5	2		ENSP00000413420.2

Frequencies

GnomAD3 genomes AF: 0.783 AC: 118673 AN: 151522 Hom.: 49471 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.783 AC: 118730 AN: 151640 Hom.: 49490 Cov.: 32 AF XY: 0.787 AC XY: 58301 AN XY: 74090

African (AFR) AF: 0.466 AC: 19270 AN: 41388

American (AMR) AF: 0.853 AC: 12930 AN: 15156

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3154 AN: 3454

East Asian (EAS) AF: 0.913 AC: 4707 AN: 5158

South Asian (SAS) AF: 0.945 AC: 4556 AN: 4822

European-Finnish (FIN) AF: 0.941 AC: 9979 AN: 10604

Middle Eastern (MID) AF: 0.928 AC: 271 AN: 292

European-Non Finnish (NFE) AF: 0.905 AC: 61309 AN: 67754

Other (OTH) AF: 0.814 AC: 1709 AN: 2100

Alfa AF: 0.837 Hom.: 6530

Bravo AF: 0.761

Asia WGS AF: 0.884 AC: 3069 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.38
PhyloP100		-0.45
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: rs835309; hg19: chr4-69682855;