Genetic Variant BTG1:c.148+355C>A (chr12-92145033-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001731.3(BTG1):c.148+355C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

35606

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

18848

African (AFR)

AF:

0.00

AC:

AN:

762

American (AMR)

AF:

0.00

AC:

AN:

500

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1240

East Asian (EAS)

AF:

0.00

AC:

AN:

1882

South Asian (SAS)

AF:

0.00

AC:

AN:

4176

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1388

Middle Eastern (MID)

AF:

0.00

AC:

AN:

186

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

23294

Other (OTH)

AF:

0.00

AC:

AN:

2178

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.60

(source)

DANN

Benign

0.61

PhyloP100

-1.0

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over