rs4583752

Variant names:

• chr4-15697382-A-G
• rs4583752
• ENST00000504598.5:n.522-8133A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-15697382-A-G
• chr4-15697382-A-T

Variant summary

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

The ENST00000504598.5(ENSG00000288606):​n.522-8133A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,018 control chromosomes in the GnomAD database, including 6,589 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 0.29 (6589 hom., cov: 32)
• Consequence: ENSG00000288606 ENST00000504598.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 9 publications found

Genes affected

ENSG00000288606 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 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
ENSG00000288606	ENST00000504598.5	n.522-8133A>G		intron_variant	Intron 3 of 3	4
ENSG00000305512	ENST00000811427.1	n.180+2193T>C		intron_variant	Intron 2 of 2
ENSG00000305512	ENST00000811428.1	n.71+2880T>C		intron_variant	Intron 1 of 1
ENSG00000305512	ENST00000811429.1	n.84+2836T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43945 AN: 151900 Hom.: 6578 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.463

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.289 AC: 43981 AN: 152018 Hom.: 6589 Cov.: 32 AF XY: 0.293 AC XY: 21760 AN XY: 74290

African (AFR) AF: 0.237 AC: 9846 AN: 41478

American (AMR) AF: 0.326 AC: 4978 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2387 AN: 5152

South Asian (SAS) AF: 0.311 AC: 1493 AN: 4804

European-Finnish (FIN) AF: 0.330 AC: 3487 AN: 10552

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19900 AN: 67968

Other (OTH) AF: 0.308 AC: 651 AN: 2114

Alfa AF: 0.293 Hom.: 10909

Bravo AF: 0.288

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.62
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs4583752; hg19: chr4-15699005;