chr4-68817137-T-G

Position:

• chr4-68817137-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
UGT2B10	NM_001075.6	c.718+400T>G		intron_variant		ENST00000265403.12	NP_001066.1
UGT2B10	NM_001144767.3	c.466+652T>G		intron_variant			NP_001138239.1
UGT2B10	NM_001290091.2	c.-26-892T>G		intron_variant			NP_001277020.1
UGT2B10	XM_017008585.3	c.718+400T>G		intron_variant			XP_016864074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT2B10	ENST00000265403.12	c.718+400T>G		intron_variant		1	NM_001075.6	ENSP00000265403	P1
UGT2B10	ENST00000458688.2	c.466+652T>G		intron_variant		2		ENSP00000413420

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

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.913

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.941

Gnomad4 NFE AF: 0.905

Gnomad4 OTH AF: 0.814

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

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

LitVar

Other links and lift over

dbSNP: rs835309; hg19: chr4-69682855;