dbSNP rs1610: UBFD1:c.*242G>A (chr16-23570832-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_019116.3(UBFD1):c.*242G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 335,370 control chromosomes in the GnomAD database, including 4,480 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 ( 1799 hom., cov: 31)

Exomes 𝑓: 0.16 ( 2681 hom. )

Consequence

UBFD1
NM_019116.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.228

Publications

22 publications found

Variant links:

Genes affected

UBFD1 (HGNC:30565): (ubiquitin family domain containing 1) Enables RNA binding activity and cadherin binding activity. [provided by Alliance of Genome Resources, Apr 2022]

UBFD1 links:

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ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019116.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBFD1	NM_019116.3	MANE Select	c.*242G>A		3_prime_UTR	Exon 7 of 7	NP_061989.2	O14562

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UBFD1	ENST00000395878.8	TSL:2 MANE Select	c.*242G>A	3_prime_UTR	Exon 7 of 7	ENSP00000379217.3	O14562
UBFD1	ENST00000926413.1		c.*242G>A	3_prime_UTR	Exon 7 of 7	ENSP00000596472.1
UBFD1	ENST00000567212.5	TSL:2	c.*242G>A	3_prime_UTR	Exon 7 of 7	ENSP00000456292.1	H3BRL3

Frequencies

GnomAD3 genomes

AF:

0.146

AC:

22090

AN:

151626

Hom.:

1797

Cov.:

show subpopulations

Gnomad AFR

AF:

0.103

Gnomad AMI

AF:

0.148

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.218

Gnomad FIN

AF:

0.223

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.135

GnomAD4 exome

AF:

0.160

AC:

29403

AN:

183624

Hom.:

2681

Cov.:

AF XY:

0.162

AC XY:

15569

AN XY:

96004

show subpopulations

African (AFR)

AF:

0.0988

AC:

550

AN:

5568

American (AMR)

AF:

0.137

AC:

890

AN:

6516

Ashkenazi Jewish (ASJ)

AF:

0.106

AC:

670

AN:

6294

East Asian (EAS)

AF:

0.292

AC:

3678

AN:

12580

South Asian (SAS)

AF:

0.201

AC:

2891

AN:

14406

European-Finnish (FIN)

AF:

0.211

AC:

2316

AN:

10984

Middle Eastern (MID)

AF:

0.132

AC:

116

AN:

878

European-Non Finnish (NFE)

AF:

0.144

AC:

16598

AN:

114934

Other (OTH)

AF:

0.148

AC:

1694

AN:

11464

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1200

2400

3601

4801

6001

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

122

244

366

488

610

<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:

0.146

AC:

22109

AN:

151746

Hom.:

1799

Cov.:

AF XY:

0.150

AC XY:

11120

AN XY:

74136

show subpopulations

African (AFR)

AF:

0.103

AC:

4258

AN:

41352

American (AMR)

AF:

0.133

AC:

2023

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

386

AN:

3464

East Asian (EAS)

AF:

0.287

AC:

1485

AN:

5168

South Asian (SAS)

AF:

0.218

AC:

1049

AN:

4806

European-Finnish (FIN)

AF:

0.223

AC:

2335

AN:

10448

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.149

AC:

10118

AN:

67946

Other (OTH)

AF:

0.140

AC:

293

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

941

1882

2822

3763

4704

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

262

524

786

1048

1310

<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:

0.141

Hom.:

2020

Bravo

AF:

0.136

Asia WGS

AF:

0.219

AC:

758

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.80

PhyloP100

0.23

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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