chr9-117702447-G-A

Position:

• chr9-117702447-G-A

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 0.531 in 152,050 control chromosomes in the GnomAD database, including 24,124 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 0.53 (24124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80777 AN: 151932 Hom.: 24131 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.653

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.531 AC: 80786 AN: 152050 Hom.: 24124 Cov.: 32 AF XY: 0.530 AC XY: 39379 AN XY: 74326

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.579

Alfa AF: 0.636 Hom.: 14425

Bravo AF: 0.527

Asia WGS AF: 0.594 AC: 2067 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1927914; hg19: chr9-120464725;