9-113378873-A-G

Variant names:

• chr9-113378873-A-G
• rs16933168

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 0.186 in 151,946 control chromosomes in the GnomAD database, including 3,127 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 0.19 (3127 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 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: 0.186 AC: 28255 AN: 151824 Hom.: 3118 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.0998

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.186 AC: 28299 AN: 151946 Hom.: 3127 Cov.: 31 AF XY: 0.184 AC XY: 13644 AN XY: 74282

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.153

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.0998

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.180

Alfa AF: 0.128 Hom.: 425

Bravo AF: 0.192

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16933168; hg19: chr9-116141153;