rs433960

Variant names:

• chr8-8910809-G-A
• rs433960
• ENST00000520582.2:n.253+7253G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-8910809-G-A
• chr8-8910809-G-C

Variant summary

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

The ENST00000520582.2(ENSG00000293372):​n.253+7253G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,074 control chromosomes in the GnomAD database, including 28,991 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 0.61 (28991 hom., cov: 33)
• Consequence: ENSG00000293372 ENST00000520582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 5 publications found

Genes affected

ENSG00000293372 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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
ENSG00000293372	ENST00000520582.2	n.253+7253G>A		intron_variant	Intron 2 of 7	3
ENSG00000293372	ENST00000753008.1	n.367+7253G>A		intron_variant	Intron 2 of 4
ENSG00000293372	ENST00000753009.1	n.427+7253G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92079 AN: 151956 Hom.: 28952 Cov.: 33

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.606 AC: 92176 AN: 152074 Hom.: 28991 Cov.: 33 AF XY: 0.612 AC XY: 45468 AN XY: 74310

African (AFR) AF: 0.454 AC: 18847 AN: 41474

American (AMR) AF: 0.718 AC: 10964 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4603 AN: 5168

South Asian (SAS) AF: 0.734 AC: 3540 AN: 4826

European-Finnish (FIN) AF: 0.636 AC: 6705 AN: 10548

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43323 AN: 67986

Other (OTH) AF: 0.616 AC: 1302 AN: 2114

Alfa AF: 0.635 Hom.: 131511

Bravo AF: 0.610

Asia WGS AF: 0.793 AC: 2757 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	0.67
DANN	Benign	0.60
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs433960; hg19: chr8-8768319;