rs1147198

Positions:

• chr9-84660433-G-T

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 0.699 in 152,058 control chromosomes in the GnomAD database, including 38,012 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 0.70 (38012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.557

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106255 AN: 151940 Hom.: 38002 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.764

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.727

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

GnomAD4 genome AF: 0.699 AC: 106319 AN: 152058 Hom.: 38012 Cov.: 32 AF XY: 0.702 AC XY: 52205 AN XY: 74336

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.729

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.706

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.803

Gnomad4 NFE AF: 0.770

Gnomad4 OTH AF: 0.725

Alfa AF: 0.750 Hom.: 19802

Bravo AF: 0.685

Asia WGS AF: 0.678 AC: 2359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1147198; hg19: chr9-87275348;