rs3133572

Variant names:

• chr8-100787575-A-C
• rs3133572
• ENST00000822399.1:n.216+2796T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-100787575-A-C
• chr8-100787575-A-T

Variant summary

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

The ENST00000822399.1(ENSG00000306981):​n.216+2796T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,002 control chromosomes in the GnomAD database, including 45,564 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 0.77 (45564 hom., cov: 30)
• Consequence: ENSG00000306981 ENST00000822399.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 2 publications found

Genes affected

ENSG00000306981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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
ENSG00000306981	ENST00000822399.1	n.216+2796T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117195 AN: 151884 Hom.: 45506 Cov.: 30

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.772 AC: 117313 AN: 152002 Hom.: 45564 Cov.: 30 AF XY: 0.771 AC XY: 57243 AN XY: 74260

African (AFR) AF: 0.857 AC: 35539 AN: 41468

American (AMR) AF: 0.807 AC: 12317 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2541 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4301 AN: 5170

South Asian (SAS) AF: 0.664 AC: 3201 AN: 4820

European-Finnish (FIN) AF: 0.701 AC: 7373 AN: 10524

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49433 AN: 67970

Other (OTH) AF: 0.776 AC: 1633 AN: 2104

Alfa AF: 0.662 Hom.: 2081

Bravo AF: 0.787

Asia WGS AF: 0.761 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.41
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs3133572; hg19: chr8-101799803;