rs1572881

Variant names:

• chr13-28641767-G-A
• rs1572881
• ENST00000784142.1:n.115-4781C>T

Variant summary

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

The ENST00000784142.1(ENSG00000289569):​n.115-4781C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,156 control chromosomes in the GnomAD database, including 2,702 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 0.17 (2702 hom., cov: 32)
• Consequence: ENSG00000289569 ENST00000784142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• Publications: 3 publications found

Genes affected

ENSG00000289569 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 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
ENSG00000289569	ENST00000784142.1	n.115-4781C>T		intron_variant	Intron 1 of 4
ENSG00000289569	ENST00000784143.1	n.103-4781C>T		intron_variant	Intron 1 of 4
ENSG00000289569	ENST00000784144.1	n.103-4781C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25360 AN: 152038 Hom.: 2690 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.167 AC: 25378 AN: 152156 Hom.: 2702 Cov.: 32 AF XY: 0.176 AC XY: 13116 AN XY: 74380

African (AFR) AF: 0.0893 AC: 3707 AN: 41532

American (AMR) AF: 0.295 AC: 4499 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3472

East Asian (EAS) AF: 0.359 AC: 1858 AN: 5176

South Asian (SAS) AF: 0.176 AC: 846 AN: 4814

European-Finnish (FIN) AF: 0.299 AC: 3157 AN: 10576

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10344 AN: 68004

Other (OTH) AF: 0.163 AC: 342 AN: 2102

Alfa AF: 0.168 Hom.: 327

Bravo AF: 0.167

Asia WGS AF: 0.289 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.4
DANN	Benign	0.71
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1572881; hg19: chr13-29215904;