12-92171542-C-G

Position:

• chr12-92171542-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000499685.2(BTG1-DT):​n.165-12584C>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 ENST00000499685.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

Genes affected

BTG1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTG1-DT	NR_135036.1	n.261-12584C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTG1-DT	ENST00000499685.2	n.165-12584C>G		intron_variant		3
BTG1-DT	ENST00000654992.1	n.143+24780C>G		intron_variant
BTG1-DT	ENST00000665784.1	n.172+24780C>G		intron_variant

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

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0872

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.106

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17251474; hg19: chr12-92565318;