chr4-68820135-G-A

Position:

• chr4-68820135-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001075.6(UGT2B10):​c.867+1958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.741 in 151,802 control chromosomes in the GnomAD database, including 45,866 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 0.74 (45866 hom., cov: 32)
• Consequence: UGT2B10 NM_001075.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGT2B10	NM_001075.6	c.867+1958G>A		intron_variant		ENST00000265403.12	NP_001066.1
UGT2B10	NM_001144767.3	c.615+1958G>A		intron_variant			NP_001138239.1
UGT2B10	NM_001290091.2	c.123+1958G>A		intron_variant			NP_001277020.1
UGT2B10	XM_017008585.3	c.867+1958G>A		intron_variant			XP_016864074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT2B10	ENST00000265403.12	c.867+1958G>A		intron_variant		1	NM_001075.6	ENSP00000265403	P1
UGT2B10	ENST00000458688.2	c.615+1958G>A		intron_variant		2		ENSP00000413420

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112456 AN: 151684 Hom.: 45858 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.902

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.892

Gnomad FIN AF: 0.929

Gnomad MID AF: 0.868

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.741 AC: 112498 AN: 151802 Hom.: 45866 Cov.: 32 AF XY: 0.745 AC XY: 55223 AN XY: 74170

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.902

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.892

Gnomad4 FIN AF: 0.929

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.767

Alfa AF: 0.814 Hom.: 11711

Bravo AF: 0.712

Asia WGS AF: 0.764 AC: 2654 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.13

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: rs835316; hg19: chr4-69685853;