9-79337213-C-T

Position:

• chr9-79337213-C-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 0.0788 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.79337213C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.0858

Gnomad4 SAS AF: 0.138

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.0638

Gnomad4 OTH AF: 0.0676

Alfa AF: 0.0620 Hom.: 432

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13292136; hg19: chr9-81952128;