rs293430

Variant names:

• chr4-68725531-A-G
• rs293430
• ENST00000789023.1:n.378+10545T>C

Variant summary

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

The ENST00000789023.1(ENSG00000302711):​n.378+10545T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 151,440 control chromosomes in the GnomAD database, including 322 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 0.036 (322 hom., cov: 32)
• Consequence: ENSG00000302711 ENST00000789023.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 0 publications found

Genes affected

ENSG00000302711 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789023.1. 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
	ENSG00000302711	ENST00000789023.1		n.378+10545T>C		intron	N/A
	ENSG00000302711	ENST00000789024.1		n.288+10545T>C		intron	N/A
	ENSG00000302711	ENST00000789025.1		n.245+10545T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0360 AC: 5448 AN: 151324 Hom.: 320 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00105

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.000427

Gnomad OTH AF: 0.0294

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

GnomAD4 genome AF: 0.0362 AC: 5481 AN: 151440 Hom.: 322 Cov.: 32 AF XY: 0.0346 AC XY: 2556 AN XY: 73928

African (AFR) AF: 0.125 AC: 5182 AN: 41332

American (AMR) AF: 0.0131 AC: 199 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 4920

South Asian (SAS) AF: 0.00105 AC: 5 AN: 4740

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10562

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.000427 AC: 29 AN: 67940

Other (OTH) AF: 0.0291 AC: 61 AN: 2098

Alfa AF: 0.0799 Hom.: 181

Bravo AF: 0.0414

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.3
DANN	Benign	0.62
PhyloP100		-0.33

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: rs293430;

hg19: chr4-69591249;