chr12-92145814-T-A

Variant names:

• chr12-92145814-T-A
• rs12694
• NM_001731.3:c.-279A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001731.3(BTG1):​c.-279A>T variant causes a 5 prime UTR 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 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.314
• Publications: 14 publications found

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

ACMG classification

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=-0.61).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001731.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG1	NM_001731.3	MANE Select	c.-279A>T		5_prime_UTR	Exon 1 of 2	NP_001722.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG1	ENST00000256015.5	TSL:1 MANE Select	c.-279A>T		5_prime_UTR	Exon 1 of 2	ENSP00000256015.3
	BTG1-DT	ENST00000501008.2	TSL:5	n.242T>A		non_coding_transcript_exon	Exon 1 of 3
	BTG1-DT	ENST00000847949.1		n.348T>A		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 101082 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 49100

African (AFR) AF: 0.00 AC: 0 AN: 3942

American (AMR) AF: 0.00 AC: 0 AN: 2818

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5384

East Asian (EAS) AF: 0.00 AC: 0 AN: 12228

South Asian (SAS) AF: 0.00 AC: 0 AN: 1074

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2816

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 598

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64560

Other (OTH) AF: 0.00 AC: 0 AN: 7662

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	5.3
DANN	Benign	0.68
PhyloP100		0.31
PromoterAI		-0.043	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs12694; hg19: chr12-92539590;