rs1998303

Variant names:

• chr9-82800066-A-G
• rs1998303

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.331

Alfa AF: 0.385 Hom.: 13519

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1998303; hg19: chr9-85414981;