rs4572353

Variant names:

• chr15-26491361-T-C
• rs4572353
• ENST00000660088.2:n.234-13449A>G

Variant summary

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

The ENST00000660088.2(ENSG00000287280):​n.234-13449A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 151,964 control chromosomes in the GnomAD database, including 15,486 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 0.44 (15486 hom., cov: 32)
• Consequence: ENSG00000287280 ENST00000660088.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902
• Publications: 5 publications found

Genes affected

ENSG00000287280 (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 (NFE) allele frequency at 95% confidence interval = 0.51 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
ENSG00000287280	ENST00000660088.2	n.234-13449A>G		intron_variant	Intron 1 of 6
ENSG00000287280	ENST00000826682.1	n.199-13449A>G		intron_variant	Intron 1 of 4
ENSG00000287280	ENST00000826683.1	n.234-13449A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66649 AN: 151846 Hom.: 15479 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.0877

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.439 AC: 66693 AN: 151964 Hom.: 15486 Cov.: 32 AF XY: 0.434 AC XY: 32268 AN XY: 74282

African (AFR) AF: 0.357 AC: 14804 AN: 41422

American (AMR) AF: 0.403 AC: 6149 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1567 AN: 3472

East Asian (EAS) AF: 0.0885 AC: 458 AN: 5176

South Asian (SAS) AF: 0.330 AC: 1591 AN: 4820

European-Finnish (FIN) AF: 0.532 AC: 5611 AN: 10538

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34981 AN: 67946

Other (OTH) AF: 0.456 AC: 963 AN: 2110

Alfa AF: 0.474 Hom.: 13052

Bravo AF: 0.427

Asia WGS AF: 0.257 AC: 899 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	0.68
DANN	Benign	0.68
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs4572353; hg19: chr15-26736508;