rs998548

Variant names:

• chr9-114512902-G-A
• rs998548

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.262 AC: 10855 AN: 41486

American (AMR) AF: 0.467 AC: 7136 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3727 AN: 5172

South Asian (SAS) AF: 0.554 AC: 2671 AN: 4822

European-Finnish (FIN) AF: 0.517 AC: 5467 AN: 10574

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37761 AN: 67998

Other (OTH) AF: 0.494 AC: 1043 AN: 2112

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
PhyloP100		-0.099

Splicing

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

Other links and lift over

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