dbSNP rs861340: UGT2B10:c.868-25G>A (chr4-68822246-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001075.6(UGT2B10):c.868-25G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 1,607,622 control chromosomes in the GnomAD database, including 611,049 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. There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.74 ( 45958 hom., cov: 31)

Exomes 𝑓: 0.88 ( 565091 hom. )

Consequence

UGT2B10
NM_001075.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.776

Publications

4 publications found

Variant links:

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]

UGT2B10 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

This position, referring to a specific DNA site, is a probable branch point but is likely benign (scored 1 / 10, using the threshold of <=3). The score ranges from 0 to 10, with values ≤3 considered benign and >5 classified as pathogenic. 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001075.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UGT2B10	NM_001075.6	MANE Select	c.868-25G>A	intron	N/A	NP_001066.1	P36537-1
UGT2B10	NM_001144767.3		c.616-25G>A	intron	N/A	NP_001138239.1	P36537-2
UGT2B10	NM_001290091.2		c.124-25G>A	intron	N/A	NP_001277020.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UGT2B10	ENST00000265403.12	TSL:1 MANE Select	c.868-25G>A	intron	N/A	ENSP00000265403.7	P36537-1
UGT2B10	ENST00000458688.2	TSL:2	c.616-25G>A	intron	N/A	ENSP00000413420.2	P36537-2
UGT2B10	ENST00000878267.1		c.868-34G>A	intron	N/A	ENSP00000548326.1

Frequencies

GnomAD3 genomes

AF:

0.742

AC:

112698

AN:

151846

Hom.:

45949

Cov.:

show subpopulations

Gnomad AFR

AF:

0.374

Gnomad AMI

AF:

0.927

Gnomad AMR

AF:

0.818

Gnomad ASJ

AF:

0.902

Gnomad EAS

AF:

0.688

Gnomad SAS

AF:

0.893

Gnomad FIN

AF:

0.929

Gnomad MID

AF:

0.867

Gnomad NFE

AF:

0.901

Gnomad OTH

AF:

0.770

GnomAD2 exomes

AF:

0.845

AC:

208674

AN:

247038

AF XY:

0.856

show subpopulations

Gnomad AFR exome

AF:

0.355

Gnomad AMR exome

AF:

0.849

Gnomad ASJ exome

AF:

0.887

Gnomad EAS exome

AF:

0.686

Gnomad FIN exome

AF:

0.929

Gnomad NFE exome

AF:

0.903

Gnomad OTH exome

AF:

0.875

GnomAD4 exome

AF:

0.876

AC:

1275645

AN:

1455658

Hom.:

565091

Cov.:

AF XY:

0.879

AC XY:

636395

AN XY:

724098

show subpopulations

African (AFR)

AF:

0.360

AC:

11888

AN:

33054

American (AMR)

AF:

0.845

AC:

36650

AN:

43360

Ashkenazi Jewish (ASJ)

AF:

0.889

AC:

23143

AN:

26020

East Asian (EAS)

AF:

0.683

AC:

27037

AN:

39596

South Asian (SAS)

AF:

0.895

AC:

76220

AN:

85196

European-Finnish (FIN)

AF:

0.927

AC:

49517

AN:

53398

Middle Eastern (MID)

AF:

0.901

AC:

3836

AN:

4258

European-Non Finnish (NFE)

AF:

0.897

AC:

996350

AN:

1110750

Other (OTH)

AF:

0.850

AC:

51004

AN:

60026

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

7831

15662

23492

31323

39154

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21264

42528

63792

85056

106320

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.742

AC:

112740

AN:

151964

Hom.:

45958

Cov.:

AF XY:

0.746

AC XY:

55367

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.374

AC:

15480

AN:

41384

American (AMR)

AF:

0.818

AC:

12465

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.902

AC:

3126

AN:

3466

East Asian (EAS)

AF:

0.689

AC:

3545

AN:

5148

South Asian (SAS)

AF:

0.893

AC:

4301

AN:

4816

European-Finnish (FIN)

AF:

0.929

AC:

9854

AN:

10608

Middle Eastern (MID)

AF:

0.861

AC:

253

AN:

294

European-Non Finnish (NFE)

AF:

0.901

AC:

61248

AN:

67990

Other (OTH)

AF:

0.768

AC:

1623

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1052

2105

3157

4210

5262

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

816

1632

2448

3264

4080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.830

Hom.:

41381

Bravo

AF:

0.713

Asia WGS

AF:

0.764

AC:

2656

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.7

(source)

DANN

Benign

0.59

PhyloP100

-0.78

BranchPoint Hunter

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over