rs731652

Variant names:

• chr12-92145033-G-A
• rs731652
• NM_001731.3:c.148+355C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-92145033-G-A
• chr12-92145033-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 2 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: 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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG1	NM_001731.3	MANE Select	c.148+355C>T		intron	N/A	NP_001722.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG1	ENST00000256015.5	TSL:1 MANE Select	c.148+355C>T		intron	N/A	ENSP00000256015.3
	BTG1-DT	ENST00000847953.1		n.134G>A		non_coding_transcript_exon	Exon 1 of 2
	BTG1	ENST00000552315.1	TSL:3	n.174+27C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23680 AN: 151902 Hom.: 1968 Cov.: 32

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.: 2 AF XY: 0.128 AC XY: 2401 AN XY: 18818

African (AFR) AF: 0.0947 AC: 72 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: 22 AN: 186

European-Non Finnish (NFE) AF: 0.131 AC: 3041 AN: 23260

Other (OTH) AF: 0.141 AC: 306 AN: 2174

GnomAD4 genome AF: 0.156 AC: 23708 AN: 152020 Hom.: 1975 Cov.: 32 AF XY: 0.157 AC XY: 11633 AN XY: 74300

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: 42 AN: 292

European-Non Finnish (NFE) AF: 0.158 AC: 10721 AN: 67942

Other (OTH) AF: 0.181 AC: 382 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.92
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)

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: rs731652; hg19: chr12-92538809;