dbSNP rs731652: BTG1:c.148+355C>T (chr12-92145033-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_001731.3(BTG1):c.148+355C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 187,566 control chromosomes in the GnomAD database, including 2,338 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 0.16 ( 1975 hom., cov: 32)

Exomes 𝑓: 0.13 ( 363 hom. )

Consequence

BTG1
NM_001731.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

2 publications found

Variant links:

Genes affected

BTG1 (HGNC:1130): (BTG anti-proliferation factor 1) This gene is a member of an anti-proliferative gene family that regulates cell growth and differentiation. Expression of this gene is highest in the G0/G1 phases of the cell cycle and downregulated when cells progressed through G1. The encoded protein interacts with several nuclear receptors, and functions as a coactivator of cell differentiation. This locus has been shown to be involved in a t(8;12)(q24;q22) chromosomal translocation in a case of B-cell chronic lymphocytic leukemia. [provided by RefSeq, Oct 2008]

BTG1 links:

BTG1-DT (HGNC:55600): (BTG1 divergent transcript)

BTG1-DT links:

Genome browser will be placed here

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=-0.86).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BTG1	NM_001731.3 link	c.148+355C>T		intron_variant	Intron 1 of 1	ENST00000256015.5	NP_001722.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
BTG1	ENST00000256015.5 link	c.148+355C>T	intron_variant	Intron 1 of 1	1	NM_001731.3	ENSP00000256015.3
BTG1-DT	ENST00000847953.1 link	n.134G>A	non_coding_transcript_exon_variant	Exon 1 of 2
BTG1	ENST00000552315.1 link	n.174+27C>T	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23680

AN:

151902

Hom.:

1968

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.150

Gnomad AMR

AF:

0.229

Gnomad ASJ

AF:

0.155

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.0976

Gnomad FIN

AF:

0.166

Gnomad MID

AF:

0.131

Gnomad NFE

AF:

0.158

Gnomad OTH

AF:

0.178

GnomAD4 exome

AF:

0.131

AC:

4667

AN:

35546

Hom.:

363

Cov.:

AF XY:

0.128

AC XY:

2401

AN XY:

18818

show subpopulations

African (AFR)

AF:

0.0947

AC:

AN:

760

American (AMR)

AF:

0.222

AC:

110

AN:

496

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

170

AN:

1232

East Asian (EAS)

AF:

0.145

AC:

272

AN:

1878

South Asian (SAS)

AF:

0.104

AC:

435

AN:

4174

European-Finnish (FIN)

AF:

0.172

AC:

239

AN:

1386

Middle Eastern (MID)

AF:

0.118

AC:

AN:

186

European-Non Finnish (NFE)

AF:

0.131

AC:

3041

AN:

23260

Other (OTH)

AF:

0.141

AC:

306

AN:

2174

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

194

389

583

778

972

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<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:

0.156

AC:

23708

AN:

152020

Hom.:

1975

Cov.:

AF XY:

0.157

AC XY:

11633

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.124

AC:

5153

AN:

41476

American (AMR)

AF:

0.230

AC:

3508

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.155

AC:

538

AN:

3468

East Asian (EAS)

AF:

0.194

AC:

1001

AN:

5150

South Asian (SAS)

AF:

0.0980

AC:

472

AN:

4814

European-Finnish (FIN)

AF:

0.166

AC:

1754

AN:

10582

Middle Eastern (MID)

AF:

0.144

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.158

AC:

10721

AN:

67942

Other (OTH)

AF:

0.181

AC:

382

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

992

1984

2977

3969

4961

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.160

Hom.:

256

Bravo

AF:

0.162

Asia WGS

AF:

0.139

AC:

485

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.92

(source)

DANN

Benign

0.86

PhyloP100

-1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over