rs4594198

Variant names:

• chr15-61585394-A-G
• rs4594198
• ENST00000559783.2:n.123+4522T>C

Variant summary

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

The ENST00000559783.2(ENSG00000259675):​n.123+4522T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,022 control chromosomes in the GnomAD database, including 15,638 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 0.43 (15638 hom., cov: 31)
• Consequence: ENSG00000259675 ENST00000559783.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.821
• Publications: 0 publications found

Genes affected

ENSG00000259675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984782	XR_001751569.2	n.235+4522T>C		intron_variant	Intron 3 of 3
LOC107984782	XR_001751570.2	n.220+4522T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259675	ENST00000559783.2	n.123+4522T>C		intron_variant	Intron 2 of 4	3
ENSG00000259675	ENST00000748013.1	n.346+4522T>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64727 AN: 151904 Hom.: 15632 Cov.: 31

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.426 AC: 64750 AN: 152022 Hom.: 15638 Cov.: 31 AF XY: 0.423 AC XY: 31451 AN XY: 74300

African (AFR) AF: 0.195 AC: 8096 AN: 41496

American (AMR) AF: 0.440 AC: 6708 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1986 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1567 AN: 5172

South Asian (SAS) AF: 0.448 AC: 2151 AN: 4806

European-Finnish (FIN) AF: 0.471 AC: 4980 AN: 10568

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37797 AN: 67950

Other (OTH) AF: 0.452 AC: 952 AN: 2106

Alfa AF: 0.472 Hom.: 2293

Bravo AF: 0.410

Asia WGS AF: 0.372 AC: 1297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.21
DANN	Benign	0.42
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs4594198; hg19: chr15-61877593;