rs16929770

Variant names:

• chr9-114512849-T-C
• rs16929770

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 0.107 in 152,284 control chromosomes in the GnomAD database, including 1,122 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 0.11 (1122 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

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 = 0.238 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: 0.107 AC: 16263 AN: 152166 Hom.: 1118 Cov.: 33

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.0441

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0732

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.107 AC: 16291 AN: 152284 Hom.: 1122 Cov.: 33 AF XY: 0.111 AC XY: 8259 AN XY: 74466

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.250

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.0441

Gnomad4 NFE AF: 0.0732

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0946 Hom.: 444

Bravo AF: 0.116

Asia WGS AF: 0.199 AC: 690 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	2.0
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16929770; hg19: chr9-117275129;