chr9-113378873-A-G

Variant names:

• chr9-113378873-A-G
• rs16933168

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 0.186 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.294 AC: 12174 AN: 41406

American (AMR) AF: 0.144 AC: 2192 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 531 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1639 AN: 5148

South Asian (SAS) AF: 0.146 AC: 702 AN: 4800

European-Finnish (FIN) AF: 0.0998 AC: 1056 AN: 10582

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9516 AN: 67972

Other (OTH) AF: 0.180 AC: 377 AN: 2098

Alfa AF: 0.151 Hom.: 858

Bravo AF: 0.192

Asia WGS AF: 0.206 AC: 714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.34
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs16933168; hg19: chr9-116141153;