rs13299822

Variant names:

• chr9-78783570-G-T
• rs13299822

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 0.0775 in 152,184 control chromosomes in the GnomAD database, including 506 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 0.077 (506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0925 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: 0.0774 AC: 11773 AN: 152066 Hom.: 505 Cov.: 32

Gnomad AFR AF: 0.0752

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0435

Gnomad FIN AF: 0.0878

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0775 AC: 11789 AN: 152184 Hom.: 506 Cov.: 32 AF XY: 0.0754 AC XY: 5609 AN XY: 74414

African (AFR) AF: 0.0752 AC: 3124 AN: 41518

American (AMR) AF: 0.0404 AC: 618 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5176

South Asian (SAS) AF: 0.0442 AC: 213 AN: 4822

European-Finnish (FIN) AF: 0.0878 AC: 930 AN: 10590

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0944 AC: 6423 AN: 68006

Other (OTH) AF: 0.0686 AC: 145 AN: 2114

Alfa AF: 0.0822 Hom.: 1057

Bravo AF: 0.0721

Asia WGS AF: 0.0240 AC: 83 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	1.0
DANN	Benign	0.31
PhyloP100		-0.097

Splicing

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

Other links and lift over

dbSNP: rs13299822; hg19: chr9-81398486;