ENST00000499685.3:n.372+9951C>T

Variant names:

• chr12-92156713-C-T
• rs2118524
• ENST00000499685.3:n.372+9951C>T

Variant summary

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

The ENST00000499685.3(BTG1-DT):​n.372+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 ENST00000499685.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 2 publications found

Genes affected

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

ENSG00000310205 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
BTG1-DT	NR_135036.1	n.260+9951C>T		intron_variant	Intron 2 of 2
BTG1-DT	NR_135037.1	n.526+7151C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BTG1-DT	ENST00000499685.3	n.372+9951C>T		intron_variant	Intron 2 of 2	3
BTG1-DT	ENST00000501008.2	n.1456+7151C>T		intron_variant	Intron 2 of 2	5
BTG1-DT	ENST00000654992.2	n.183+9951C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.0476 AC: 1976 AN: 41514

American (AMR) AF: 0.133 AC: 2036 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3470

East Asian (EAS) AF: 0.00231 AC: 12 AN: 5188

South Asian (SAS) AF: 0.0801 AC: 386 AN: 4820

European-Finnish (FIN) AF: 0.184 AC: 1947 AN: 10610

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14847 AN: 67996

Other (OTH) AF: 0.160 AC: 338 AN: 2112

Alfa AF: 0.195 Hom.: 1700

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs2118524; hg19: chr12-92550489;