rs439401

Variant names:

• chr19-44911194-T-C
• rs439401
• ENST00000623895.1:n.1820T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: drug response no assertion criteria provided O:1
• Conservation: PhyloP100: -0.0130

Genes affected

ENSG00000280087 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	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.: 33

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

Gnomad4 AFR exome AF: 1.00 AC: 4 AN: 4

Gnomad4 AMR exome AF: 1.00 AC: 2 AN: 2

Gnomad4 ASJ exome AF: 0.750 AC: 3 AN: 4

Gnomad4 EAS exome AF: 0.500 AC: 5 AN: 10

Gnomad4 SAS exome AC: 0 AN: 0

Gnomad4 FIN exome AF: 1.00 AC: 2 AN: 2

Gnomad4 NFE exome AF: 0.722 AC: 104 AN: 144

Gnomad4 Remaining exome AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.670 AC: 101979 AN: 152164 Hom.: 35477 Cov.: 33 AF XY: 0.667 AC XY: 49620 AN XY: 74390

Gnomad4 AFR AF: 0.853 AC: 0.8527 AN: 0.8527

Gnomad4 AMR AF: 0.502 AC: 0.501506 AN: 0.501506

Gnomad4 ASJ AF: 0.574 AC: 0.573529 AN: 0.573529

Gnomad4 EAS AF: 0.422 AC: 0.421572 AN: 0.421572

Gnomad4 SAS AF: 0.442 AC: 0.442371 AN: 0.442371

Gnomad4 FIN AF: 0.727 AC: 0.726981 AN: 0.726981

Gnomad4 NFE AF: 0.629 AC: 0.629425 AN: 0.629425

Gnomad4 OTH AF: 0.643 AC: 0.643466 AN: 0.643466

Alfa AF: 0.632 Hom.: 144864

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

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

Other links and lift over

dbSNP: rs439401; hg19: chr19-45414451;