rs1597390

Variant names:

• chr3-143156206-C-A
• rs1597390
• ENST00000840693.1:n.84-8949G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-143156206-C-A
• chr3-143156206-C-T

Variant summary

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

The ENST00000840693.1(ENSG00000309389):​n.84-8949G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,990 control chromosomes in the GnomAD database, including 8,505 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 0.31 (8505 hom., cov: 33)
• Consequence: ENSG00000309389 ENST00000840693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 1 publications found

Genes affected

ENSG00000309389 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840693.1. 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
	ENSG00000309389	ENST00000840693.1		n.84-8949G>T		intron	N/A
	ENSG00000309389	ENST00000840694.1		n.65-2055G>T		intron	N/A
	ENSG00000309389	ENST00000840695.1		n.63-1916G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46586 AN: 151872 Hom.: 8476 Cov.: 33

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.284

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.307 AC: 46668 AN: 151990 Hom.: 8505 Cov.: 33 AF XY: 0.308 AC XY: 22843 AN XY: 74266

African (AFR) AF: 0.511 AC: 21191 AN: 41442

American (AMR) AF: 0.260 AC: 3977 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3468

East Asian (EAS) AF: 0.195 AC: 1008 AN: 5168

South Asian (SAS) AF: 0.332 AC: 1602 AN: 4822

European-Finnish (FIN) AF: 0.258 AC: 2723 AN: 10548

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14681 AN: 67954

Other (OTH) AF: 0.289 AC: 611 AN: 2112

Alfa AF: 0.145 Hom.: 277

Bravo AF: 0.317

Asia WGS AF: 0.318 AC: 1107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.47
PhyloP100		-0.39

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: rs1597390;

hg19: chr3-142875048;