9-29767805-C-G

Variant names:

• chr9-29767805-C-G
• rs16915269

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 0.167 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.166 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

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.0921

Gnomad4 ASJ AF: 0.0666

Gnomad4 EAS AF: 0.0571

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.0964

Gnomad4 NFE AF: 0.0812

Gnomad4 OTH AF: 0.132

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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