chr9-117676199-T-C

Position:

• chr9-117676199-T-C

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 0.75 in 151,708 control chromosomes in the GnomAD database, including 44,450 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 0.75 (44450 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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 = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.117676199T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113688 AN: 151588 Hom.: 44428 Cov.: 31

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.750 AC: 113758 AN: 151708 Hom.: 44450 Cov.: 31 AF XY: 0.748 AC XY: 55487 AN XY: 74168

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.845

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.872

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.860

Gnomad4 OTH AF: 0.785

Alfa AF: 0.794 Hom.: 6028

Bravo AF: 0.747

Asia WGS AF: 0.813 AC: 2829 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1329060; hg19: chr9-120438477;