rs1519568

Variant names:

• chr3-154522700-T-C
• rs1519568
• ENST00000498604.1:n.45-10931A>G

Variant summary

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

The ENST00000498604.1(ENSG00000243861):​n.45-10931A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,090 control chromosomes in the GnomAD database, including 4,385 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 0.20 (4385 hom., cov: 32)
• Consequence: ENSG00000243861 ENST00000498604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 3 publications found

Genes affected

ENSG00000243861 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 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
ENSG00000243861	ENST00000498604.1	n.45-10931A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30419 AN: 151972 Hom.: 4363 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.0649

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.201 AC: 30494 AN: 152090 Hom.: 4385 Cov.: 32 AF XY: 0.195 AC XY: 14515 AN XY: 74352

African (AFR) AF: 0.410 AC: 17014 AN: 41454

American (AMR) AF: 0.150 AC: 2286 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 330 AN: 3466

East Asian (EAS) AF: 0.0645 AC: 333 AN: 5162

South Asian (SAS) AF: 0.147 AC: 711 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10592

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.118 AC: 8058 AN: 68008

Other (OTH) AF: 0.189 AC: 399 AN: 2114

Alfa AF: 0.141 Hom.: 8287

Bravo AF: 0.212

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.79
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs1519568; hg19: chr3-154240489;