rs790455

Variant names:

• chr12-92221589-G-T
• rs790455
• ENST00000654992.2:n.452-3199G>T

Variant summary

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

The ENST00000654992.2(BTG1-DT):​n.452-3199G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,032 control chromosomes in the GnomAD database, including 20,310 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 0.51 (20310 hom., cov: 32)
• Consequence: BTG1-DT ENST00000654992.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 8 publications found

Genes affected

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654992.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG1-DT	ENST00000654992.2		n.452-3199G>T		intron	N/A
	BTG1-DT	ENST00000665784.1		n.441-3199G>T		intron	N/A
	BTG1-DT	ENST00000847927.1		n.552+474G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77910 AN: 151914 Hom.: 20288 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.526

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

GnomAD4 genome AF: 0.513 AC: 77966 AN: 152032 Hom.: 20310 Cov.: 32 AF XY: 0.516 AC XY: 38372 AN XY: 74296

African (AFR) AF: 0.425 AC: 17617 AN: 41446

American (AMR) AF: 0.584 AC: 8926 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2018 AN: 3470

East Asian (EAS) AF: 0.496 AC: 2554 AN: 5154

South Asian (SAS) AF: 0.592 AC: 2860 AN: 4830

European-Finnish (FIN) AF: 0.544 AC: 5737 AN: 10550

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.539 AC: 36641 AN: 67982

Other (OTH) AF: 0.528 AC: 1116 AN: 2114

Alfa AF: 0.533 Hom.: 95223

Bravo AF: 0.509

Asia WGS AF: 0.516 AC: 1795 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.68
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs790455; hg19: chr12-92615365;