dbSNP rs439401: ENSG00000280087:n.1820T>C (chr19-44911194-T-C) – ACMG Classification: Benign (-12 pts)

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

Clinical Significance

drug response no assertion criteria provided O:1

Conservation

PhyloP100: -0.0130

Variant links:

Genes affected

ENSG00000280087 (HGNC:):

ENSG00000280087 links:

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
ENSG00000280087	ENST00000623895.1 link	n.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.:

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.:

Cov.:

AF XY:

0.714

AC XY:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over