rs998548

Positions:

• chr9-114512902-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;