rs2118524

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.662
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

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-DTNR_135036.1 linkuse as main transcriptn.260+9951C>T intron_variant
BTG1-DTNR_135037.1 linkuse as main transcriptn.526+7151C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BTG1-DTENST00000499685.2 linkuse as main transcriptn.164+9951C>T intron_variant 3
BTG1-DTENST00000501008.2 linkuse as main transcriptn.1456+7151C>T intron_variant 5
BTG1-DTENST00000654992.1 linkuse as main transcriptn.143+9951C>T intron_variant
BTG1-DTENST00000665784.1 linkuse as main transcriptn.172+9951C>T intron_variant

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2118524; hg19: chr12-92550489; API