chr9-29767805-C-G

Variant names:

• chr9-29767805-C-G
• rs16915269

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 0.167 in 152,032 control chromosomes in the GnomAD database, including 3,423 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 0.17 (3423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25261 AN: 151914 Hom.: 3409 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0917

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0571

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0964

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0812

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.167 AC: 25323 AN: 152032 Hom.: 3423 Cov.: 32 AF XY: 0.165 AC XY: 12278 AN XY: 74312

African (AFR) AF: 0.379 AC: 15689 AN: 41444

American (AMR) AF: 0.0921 AC: 1406 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3468

East Asian (EAS) AF: 0.0571 AC: 295 AN: 5168

South Asian (SAS) AF: 0.171 AC: 825 AN: 4822

European-Finnish (FIN) AF: 0.0964 AC: 1019 AN: 10574

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0812 AC: 5521 AN: 67980

Other (OTH) AF: 0.132 AC: 279 AN: 2112

Alfa AF: 0.0369 Hom.: 36

Bravo AF: 0.172

Asia WGS AF: 0.121 AC: 423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.20
PhyloP100		-0.022

Splicing

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

Other links and lift over

dbSNP: rs16915269; hg19: chr9-29767803; COSMIC: COSV60349224;