chr9-84660433-G-T

Variant names:

• chr9-84660433-G-T
• rs1147198

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 0.699 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
• Publications: 18 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.533 AC: 22114 AN: 41466

American (AMR) AF: 0.729 AC: 11136 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2661 AN: 3466

East Asian (EAS) AF: 0.706 AC: 3648 AN: 5168

South Asian (SAS) AF: 0.730 AC: 3508 AN: 4806

European-Finnish (FIN) AF: 0.803 AC: 8486 AN: 10574

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52329 AN: 67986

Other (OTH) AF: 0.725 AC: 1531 AN: 2112

Alfa AF: 0.739 Hom.: 27859

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1147198; hg19: chr9-87275348;