rs439401

Variant summary

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

The ENST00000623895.1(ENSG00000280087):​n.1820T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.67 in 152,334 control chromosomes in the GnomAD database, including 35,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (no stars).

Frequency

Genomes: 𝑓 0.67 ( 35477 hom., cov: 33)
Exomes 𝑓: 0.72 ( 44 hom. )

Consequence

ENSG00000280087
ENST00000623895.1 non_coding_transcript_exon

Scores

2

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: -0.0130
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=-0.66).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000280087ENST00000623895.1 linkn.1820T>C non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.670
AC:
101854
AN:
152046
Hom.:
35420
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.853
Gnomad AMI
AF:
0.657
Gnomad AMR
AF:
0.501
Gnomad ASJ
AF:
0.574
Gnomad EAS
AF:
0.421
Gnomad SAS
AF:
0.442
Gnomad FIN
AF:
0.727
Gnomad MID
AF:
0.500
Gnomad NFE
AF:
0.629
Gnomad OTH
AF:
0.639
GnomAD4 exome
AF:
0.718
AC:
122
AN:
170
Hom.:
44
Cov.:
0
AF XY:
0.714
AC XY:
90
AN XY:
126
show subpopulations
Gnomad4 AFR exome
AF:
1.00
Gnomad4 AMR exome
AF:
1.00
Gnomad4 ASJ exome
AF:
0.750
Gnomad4 EAS exome
AF:
0.500
Gnomad4 FIN exome
AF:
1.00
Gnomad4 NFE exome
AF:
0.722
Gnomad4 OTH exome
AF:
0.500
GnomAD4 genome
AF:
0.670
AC:
101979
AN:
152164
Hom.:
35477
Cov.:
33
AF XY:
0.667
AC XY:
49620
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.853
Gnomad4 AMR
AF:
0.502
Gnomad4 ASJ
AF:
0.574
Gnomad4 EAS
AF:
0.422
Gnomad4 SAS
AF:
0.442
Gnomad4 FIN
AF:
0.727
Gnomad4 NFE
AF:
0.629
Gnomad4 OTH
AF:
0.643
Alfa
AF:
0.621
Hom.:
66547
Bravo
AF:
0.663
Asia WGS
AF:
0.540
AC:
1880
AN:
3478

ClinVar

Significance: drug response
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Warfarin response Other:1
Aug 31, 2010
Pharmacogenomics Lab, Chungbuk National University
Significance: drug response
Review Status: no assertion criteria provided
Collection Method: research

- likely responsive

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.66
CADD
Benign
4.9
DANN
Benign
0.67

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: rs439401; hg19: chr19-45414451; API