1-203302802-G-T

Variant summary

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

The NR_034150.1(BTG2-DT):​n.474-1521C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,122 control chromosomes in the GnomAD database, including 10,557 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 0.35 ( 10557 hom., cov: 33)

Consequence

BTG2-DT
NR_034150.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.369
Variant links:
Genes affected
BTG2-DT (HGNC:49452): (BTG2 divergent transcript)

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=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
BTG2-DTNR_034150.1 linkuse as main transcriptn.474-1521C>A intron_variant, non_coding_transcript_variant
BTG2-DTNR_034151.1 linkuse as main transcriptn.660-1521C>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
BTG2-DTENST00000457348.5 linkuse as main transcriptn.458-1521C>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.348
AC:
52873
AN:
152004
Hom.:
10554
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.162
Gnomad AMI
AF:
0.481
Gnomad AMR
AF:
0.311
Gnomad ASJ
AF:
0.470
Gnomad EAS
AF:
0.217
Gnomad SAS
AF:
0.368
Gnomad FIN
AF:
0.448
Gnomad MID
AF:
0.424
Gnomad NFE
AF:
0.454
Gnomad OTH
AF:
0.357
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.348
AC:
52887
AN:
152122
Hom.:
10557
Cov.:
33
AF XY:
0.347
AC XY:
25772
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.162
Gnomad4 AMR
AF:
0.310
Gnomad4 ASJ
AF:
0.470
Gnomad4 EAS
AF:
0.217
Gnomad4 SAS
AF:
0.367
Gnomad4 FIN
AF:
0.448
Gnomad4 NFE
AF:
0.454
Gnomad4 OTH
AF:
0.361
Alfa
AF:
0.431
Hom.:
27634
Bravo
AF:
0.328
Asia WGS
AF:
0.307
AC:
1065
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
8.6
DANN
Benign
0.72

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: rs12136280; hg19: chr1-203271930; API