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
• Publications: 234 publications found

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000623895.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000280087	ENST00000623895.1	TSL:6	n.1820T>C		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AF: 1.00 AC: 4 AN: 4

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 0.500 AC: 5 AN: 10

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.722 AC: 104 AN: 144

Other (OTH) 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

African (AFR) AF: 0.853 AC: 35428 AN: 41548

American (AMR) AF: 0.502 AC: 7660 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1989 AN: 3468

East Asian (EAS) AF: 0.422 AC: 2177 AN: 5164

South Asian (SAS) AF: 0.442 AC: 2134 AN: 4824

European-Finnish (FIN) AF: 0.727 AC: 7706 AN: 10600

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42782 AN: 67970

Other (OTH) AF: 0.643 AC: 1359 AN: 2112

Alfa AF: 0.632 Hom.: 144864

Bravo AF: 0.663

Asia WGS AF: 0.540 AC: 1880 AN: 3478

ClinVar

ClinVar submissions

Significance: drug response

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Warfarin response (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	4.9
DANN	Benign	0.67
PhyloP100		-0.013

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs439401;

hg19: chr19-45414451;