1-203302802-G-T

Variant names:

• chr1-203302802-G-T
• rs12136280
• ENST00000425698.3:n.417-1521C>A

Variant summary

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

The ENST00000457348.5(BTG2-DT):​n.458-1521C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,122 control chromosomes in the GnomAD database, including 10,557 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 0.35 (10557 hom., cov: 33)
• Consequence: BTG2-DT ENST00000457348.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 3 publications found

Genes affected

BTG2-DT (HGNC:49452): (BTG2 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 (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457348.5. 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
	BTG2-DT	NR_034150.1		n.474-1521C>A		intron	N/A
	BTG2-DT	NR_034151.1		n.660-1521C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG2-DT	ENST00000425698.3	TSL:3	n.417-1521C>A		intron	N/A
	BTG2-DT	ENST00000432511.4	TSL:3	n.446-1521C>A		intron	N/A
	BTG2-DT	ENST00000457348.5	TSL:2	n.458-1521C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52873 AN: 152004 Hom.: 10554 Cov.: 33

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.357

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.348 AC: 52887 AN: 152122 Hom.: 10557 Cov.: 33 AF XY: 0.347 AC XY: 25772 AN XY: 74338

African (AFR) AF: 0.162 AC: 6735 AN: 41530

American (AMR) AF: 0.310 AC: 4747 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1631 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1126 AN: 5180

South Asian (SAS) AF: 0.367 AC: 1774 AN: 4828

European-Finnish (FIN) AF: 0.448 AC: 4715 AN: 10526

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30838 AN: 67980

Other (OTH) AF: 0.361 AC: 764 AN: 2114

Alfa AF: 0.420 Hom.: 55664

Bravo AF: 0.328

Asia WGS AF: 0.307 AC: 1065 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	8.6
DANN	Benign	0.72
PhyloP100		0.37

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12136280;

hg19: chr1-203271930;