3-139495628-A-T

Variant summary

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

The NR_121609.1(COPB2-DT):​n.354+72514A>T variant causes a intron, non coding transcript change. The variant allele was found at a frequency of 0.151 in 151,590 control chromosomes in the GnomAD database, including 3,823 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 ( 3823 hom., cov: 31)

Consequence

COPB2-DT
NR_121609.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.73
Variant links:
Genes affected
COPB2-DT (HGNC:55579): (COPB2 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=-0.64).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
COPB2-DTNR_121609.1 linkuse as main transcriptn.354+72514A>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
COPB2-DTENST00000658348.1 linkuse as main transcriptn.671+72514A>T intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.151
AC:
22864
AN:
151476
Hom.:
3816
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0453
Gnomad AMI
AF:
0.0859
Gnomad AMR
AF:
0.338
Gnomad ASJ
AF:
0.0897
Gnomad EAS
AF:
0.858
Gnomad SAS
AF:
0.274
Gnomad FIN
AF:
0.189
Gnomad MID
AF:
0.0696
Gnomad NFE
AF:
0.110
Gnomad OTH
AF:
0.141
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.151
AC:
22880
AN:
151590
Hom.:
3823
Cov.:
31
AF XY:
0.164
AC XY:
12166
AN XY:
74082
show subpopulations
Gnomad4 AFR
AF:
0.0453
Gnomad4 AMR
AF:
0.339
Gnomad4 ASJ
AF:
0.0897
Gnomad4 EAS
AF:
0.857
Gnomad4 SAS
AF:
0.275
Gnomad4 FIN
AF:
0.189
Gnomad4 NFE
AF:
0.110
Gnomad4 OTH
AF:
0.142
Alfa
AF:
0.123
Hom.:
237
Bravo
AF:
0.165
Asia WGS
AF:
0.499
AC:
1731
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
CADD
Benign
9.6
DANN
Benign
0.74

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: rs2165139; hg19: chr3-139214470; API