12-92171542-C-G

Variant names:

• chr12-92171542-C-G
• rs17251474
• ENST00000499685.3:n.373-12584C>G

Variant summary

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

The ENST00000499685.3(BTG1-DT):​n.373-12584C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,096 control chromosomes in the GnomAD database, including 1,376 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 0.13 (1376 hom., cov: 32)
• Consequence: BTG1-DT ENST00000499685.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.209 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.261-12584C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BTG1-DT	ENST00000499685.3	TSL:3	n.373-12584C>G		intron	N/A
	BTG1-DT	ENST00000654992.2		n.183+24780C>G		intron	N/A
	BTG1-DT	ENST00000665784.1		n.172+24780C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19488 AN: 151978 Hom.: 1378 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0874

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.128 AC: 19495 AN: 152096 Hom.: 1376 Cov.: 32 AF XY: 0.128 AC XY: 9483 AN XY: 74354

African (AFR) AF: 0.155 AC: 6411 AN: 41468

American (AMR) AF: 0.0872 AC: 1333 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3470

East Asian (EAS) AF: 0.220 AC: 1139 AN: 5186

South Asian (SAS) AF: 0.107 AC: 518 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1407 AN: 10564

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7982 AN: 67978

Other (OTH) AF: 0.106 AC: 223 AN: 2110

Alfa AF: 0.0648 Hom.: 71

Bravo AF: 0.127

Asia WGS AF: 0.138 AC: 479 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs17251474; hg19: chr12-92565318;