rs9329223

Variant names:

• chr8-10474244-A-G
• rs9329223
• ENST00000843329.1:n.212+4934T>C

Variant summary

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

The ENST00000843329.1(ENSG00000253678):​n.212+4934T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,958 control chromosomes in the GnomAD database, including 26,645 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 0.59 (26645 hom., cov: 32)
• Consequence: ENSG00000253678 ENST00000843329.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 7 publications found

Genes affected

ENSG00000253678 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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
ENSG00000253678	ENST00000843329.1	n.212+4934T>C		intron_variant	Intron 1 of 1
ENSG00000253678	ENST00000843330.1	n.212+4934T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.586 AC: 89022 AN: 151840 Hom.: 26628 Cov.: 32

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.586 AC: 89086 AN: 151958 Hom.: 26645 Cov.: 32 AF XY: 0.595 AC XY: 44189 AN XY: 74254

African (AFR) AF: 0.527 AC: 21865 AN: 41454

American (AMR) AF: 0.686 AC: 10475 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3468

East Asian (EAS) AF: 0.870 AC: 4506 AN: 5180

South Asian (SAS) AF: 0.723 AC: 3477 AN: 4806

European-Finnish (FIN) AF: 0.612 AC: 6436 AN: 10524

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.567 AC: 38528 AN: 67934

Other (OTH) AF: 0.586 AC: 1237 AN: 2110

Alfa AF: 0.577 Hom.: 63982

Bravo AF: 0.592

Asia WGS AF: 0.783 AC: 2723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.62
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9329223; hg19: chr8-10331754;