dbSNP rs16405: BTRC:c.*840_*848delAACAGTGGA (chr10-101553962-CAACAGTGGA-C) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_033637.4(BTRC):c.*840_*848delAACAGTGGA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,084 control chromosomes in the GnomAD database, including 9,719 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.32 ( 9714 hom., cov: 0)

Exomes 𝑓: 0.20 ( 5 hom. )

Consequence

BTRC
NM_033637.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.97

Publications

12 publications found

Variant links:

Genes affected

BTRC (HGNC:1144): (beta-transducin repeat containing E3 ubiquitin protein ligase) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbws class; in addition to an F-box, this protein contains multiple WD-40 repeats. The encoded protein mediates degradation of CD4 via its interaction with HIV-1 Vpu. It has also been shown to ubiquitinate phosphorylated NFKBIA (nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha), targeting it for degradation and thus activating nuclear factor kappa-B. Alternatively spliced transcript variants have been described. A related pseudogene exists in chromosome 6. [provided by RefSeq, Mar 2012]

BTRC links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTRC	NM_033637.4 link	c.840_848delAACAGTGGA		3_prime_UTR_variant	Exon 15 of 15	ENST00000370187.8	NP_378663.1	Q9Y297-1A0A0S2Z4P6B2R8L3Q68DS0

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
BTRC	ENST00000370187.8 link	c.840_848delAACAGTGGA	3_prime_UTR_variant	Exon 15 of 15	1	NM_033637.4	ENSP00000359206.3	Q9Y297-1
BTRC	ENST00000393441.8 link	c.840_848delAACAGTGGA	3_prime_UTR_variant	Exon 14 of 14	1		ENSP00000377088.5	B7Z3H4
BTRC	ENST00000408038.6 link	c.840_848delAACAGTGGA	3_prime_UTR_variant	Exon 14 of 14	1		ENSP00000385339.2	Q9Y297-2

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

47959

AN:

151688

Hom.:

9703

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.0296

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.660

Gnomad SAS

AF:

0.328

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.161

Gnomad NFE

AF:

0.187

Gnomad OTH

AF:

0.308

GnomAD4 exome

AF:

0.203

AC:

AN:

276

Hom.:

AF XY:

0.215

AC XY:

AN XY:

172

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.200

AC:

AN:

260

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.400

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.468

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.316

AC:

48008

AN:

151808

Hom.:

9714

Cov.:

AF XY:

0.317

AC XY:

23547

AN XY:

74200

show subpopulations

African (AFR)

AF:

0.541

AC:

22325

AN:

41290

American (AMR)

AF:

0.287

AC:

4383

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

752

AN:

3470

East Asian (EAS)

AF:

0.659

AC:

3378

AN:

5124

South Asian (SAS)

AF:

0.328

AC:

1581

AN:

4818

European-Finnish (FIN)

AF:

0.206

AC:

2178

AN:

10566

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.187

AC:

12690

AN:

67976

Other (OTH)

AF:

0.306

AC:

644

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

1359

2718

4078

5437

6796

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<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:

0.258

Hom.:

781

Bravo

AF:

0.333

Asia WGS

AF:

0.456

AC:

1582

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

2.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over