rs9567731

Variant names:

• chr13-46826551-A-G
• rs9567731
• ENST00000783844.1:n.96-4745A>G

Variant summary

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

The ENST00000783844.1(ENSG00000302073):​n.96-4745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 152,188 control chromosomes in the GnomAD database, including 45,805 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 (45805 hom., cov: 33)
• Consequence: ENSG00000302073 ENST00000783844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• Publications: 6 publications found

Genes affected

ENSG00000302073 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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
ENSG00000302073	ENST00000783844.1	n.96-4745A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117113 AN: 152070 Hom.: 45775 Cov.: 33

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.770 AC: 117195 AN: 152188 Hom.: 45805 Cov.: 33 AF XY: 0.762 AC XY: 56681 AN XY: 74382

African (AFR) AF: 0.900 AC: 37392 AN: 41552

American (AMR) AF: 0.745 AC: 11387 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2768 AN: 3468

East Asian (EAS) AF: 0.733 AC: 3799 AN: 5186

South Asian (SAS) AF: 0.588 AC: 2836 AN: 4826

European-Finnish (FIN) AF: 0.633 AC: 6698 AN: 10582

Middle Eastern (MID) AF: 0.709 AC: 207 AN: 292

European-Non Finnish (NFE) AF: 0.733 AC: 49840 AN: 67972

Other (OTH) AF: 0.774 AC: 1637 AN: 2116

Alfa AF: 0.751 Hom.: 62799

Bravo AF: 0.791

Asia WGS AF: 0.666 AC: 2319 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.61
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs9567731; hg19: chr13-47400686;