rs1998303

Variant names:

• chr9-82800066-A-G
• rs1998303
• ENST00000792604.1:n.354+30972T>C

Variant summary

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

The ENST00000792604.1(ENSG00000303186):​n.354+30972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 151,898 control chromosomes in the GnomAD database, including 10,520 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 0.37 (10520 hom., cov: 32)
• Consequence: ENSG00000303186 ENST00000792604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660
• Publications: 12 publications found

Genes affected

ENSG00000303186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.478 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
ENSG00000303186	ENST00000792604.1	n.354+30972T>C		intron_variant	Intron 4 of 4
ENSG00000303186	ENST00000792605.1	n.202-17684T>C		intron_variant	Intron 2 of 3
ENSG00000303186	ENST00000792606.1	n.163+30972T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56326 AN: 151780 Hom.: 10521 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.371 AC: 56325 AN: 151898 Hom.: 10520 Cov.: 32 AF XY: 0.369 AC XY: 27352 AN XY: 74224

African (AFR) AF: 0.337 AC: 13970 AN: 41434

American (AMR) AF: 0.344 AC: 5233 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2541 AN: 5142

South Asian (SAS) AF: 0.359 AC: 1727 AN: 4812

European-Finnish (FIN) AF: 0.360 AC: 3803 AN: 10560

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26495 AN: 67932

Other (OTH) AF: 0.331 AC: 698 AN: 2110

Alfa AF: 0.384 Hom.: 19684

Bravo AF: 0.367

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.44
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs1998303; hg19: chr9-85414981;