rs998548

Variant names:

• chr9-114512902-G-A
• rs998548

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 0.466 in 152,128 control chromosomes in the GnomAD database, including 17,874 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 0.47 (17874 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 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: 0.466 AC: 70896 AN: 152010 Hom.: 17857 Cov.: 33

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.466 AC: 70938 AN: 152128 Hom.: 17874 Cov.: 33 AF XY: 0.466 AC XY: 34687 AN XY: 74364

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.494

Alfa AF: 0.498 Hom.: 3310

Bravo AF: 0.455

Asia WGS AF: 0.634 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs998548; hg19: chr9-117275182; COSMIC: COSV60395454;