9-79337213-C-T

Variant names:

• chr9-79337213-C-T
• rs13292136

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 0.0788 in 152,184 control chromosomes in the GnomAD database, including 529 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 0.079 (529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 106 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.129 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: 0.0787 AC: 11961 AN: 152066 Hom.: 523 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.0991

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0854

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0638

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0788 AC: 11988 AN: 152184 Hom.: 529 Cov.: 32 AF XY: 0.0820 AC XY: 6104 AN XY: 74398

African (AFR) AF: 0.0762 AC: 3165 AN: 41532

American (AMR) AF: 0.111 AC: 1692 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3468

East Asian (EAS) AF: 0.0858 AC: 444 AN: 5174

South Asian (SAS) AF: 0.138 AC: 666 AN: 4820

European-Finnish (FIN) AF: 0.130 AC: 1373 AN: 10596

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0638 AC: 4335 AN: 67992

Other (OTH) AF: 0.0676 AC: 143 AN: 2114

Alfa AF: 0.0666 Hom.: 1189

Bravo AF: 0.0769

Asia WGS AF: 0.113 AC: 394 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.9
DANN	Benign	0.26
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs13292136; hg19: chr9-81952128;