rs2118524

Positions:

• chr12-92156713-C-T

Variant summary

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

The ENST00000499685.2(BTG1-DT):​n.164+9951C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,208 control chromosomes in the GnomAD database, including 2,050 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 0.15 (2050 hom., cov: 32)
• Consequence: BTG1-DT ENST00000499685.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

Genes affected

BTG1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTG1-DT	NR_135036.1	n.260+9951C>T		intron_variant
BTG1-DT	NR_135037.1	n.526+7151C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BTG1-DT	ENST00000499685.2	n.164+9951C>T		intron_variant		3
BTG1-DT	ENST00000501008.2	n.1456+7151C>T		intron_variant		5
BTG1-DT	ENST00000654992.1	n.143+9951C>T		intron_variant
BTG1-DT	ENST00000665784.1	n.172+9951C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22394 AN: 152090 Hom.: 2053 Cov.: 32

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.147 AC: 22391 AN: 152208 Hom.: 2050 Cov.: 32 AF XY: 0.143 AC XY: 10668 AN XY: 74418

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.00231

Gnomad4 SAS AF: 0.0801

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.160

Alfa AF: 0.195 Hom.: 1532

Bravo AF: 0.139

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2118524; hg19: chr12-92550489;