rs709228

Variant names:

• chr12-92178653-G-T
• rs709228
• ENST00000499685.3:n.373-5473G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000499685.3(BTG1-DT):​n.373-5473G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,034 control chromosomes in the GnomAD database, including 8,679 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 0.33 (8679 hom., cov: 32)
• Consequence: BTG1-DT ENST00000499685.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499685.3. 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-DT	NR_135036.1		n.261-5473G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG1-DT	ENST00000499685.3	TSL:3	n.373-5473G>T		intron	N/A
	BTG1-DT	ENST00000654992.2		n.183+31891G>T		intron	N/A
	BTG1-DT	ENST00000665784.1		n.172+31891G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49780 AN: 151918 Hom.: 8667 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.328 AC: 49847 AN: 152034 Hom.: 8679 Cov.: 32 AF XY: 0.323 AC XY: 24008 AN XY: 74316

African (AFR) AF: 0.444 AC: 18398 AN: 41452

American (AMR) AF: 0.315 AC: 4808 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1106 AN: 5186

South Asian (SAS) AF: 0.196 AC: 945 AN: 4818

European-Finnish (FIN) AF: 0.281 AC: 2970 AN: 10556

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19678 AN: 67968

Other (OTH) AF: 0.330 AC: 697 AN: 2114

Alfa AF: 0.301 Hom.: 12132

Bravo AF: 0.338

Asia WGS AF: 0.217 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.79
PhyloP100		1.5

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: rs709228;

hg19: chr12-92572429;