rs9298203

Variant names:

• chr8-72195487-C-G
• rs9298203
• ENST00000803291.1:n.275-31412C>G

Variant summary

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

The ENST00000803291.1(ENSG00000304428):​n.275-31412C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,982 control chromosomes in the GnomAD database, including 13,412 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 0.42 (13412 hom., cov: 33)
• Consequence: ENSG00000304428 ENST00000803291.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 3 publications found

Genes affected

ENSG00000304428 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 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
ENSG00000304428	ENST00000803291.1	n.275-31412C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63281 AN: 151864 Hom.: 13401 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.417 AC: 63332 AN: 151982 Hom.: 13412 Cov.: 33 AF XY: 0.418 AC XY: 31054 AN XY: 74300

African (AFR) AF: 0.341 AC: 14105 AN: 41424

American (AMR) AF: 0.418 AC: 6388 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1662 AN: 3470

East Asian (EAS) AF: 0.400 AC: 2063 AN: 5162

South Asian (SAS) AF: 0.447 AC: 2155 AN: 4820

European-Finnish (FIN) AF: 0.494 AC: 5211 AN: 10540

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30401 AN: 67964

Other (OTH) AF: 0.412 AC: 870 AN: 2110

Alfa AF: 0.426 Hom.: 1745

Bravo AF: 0.406

Asia WGS AF: 0.411 AC: 1425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.68
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9298203; hg19: chr8-73107722;