rs16929770

Variant names:

• chr9-114512849-T-C
• rs16929770

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 0.107 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
• Publications: 1 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 = 0.238 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.112 AC: 4665 AN: 41556

American (AMR) AF: 0.179 AC: 2739 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1293 AN: 5176

South Asian (SAS) AF: 0.230 AC: 1111 AN: 4820

European-Finnish (FIN) AF: 0.0441 AC: 469 AN: 10626

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0732 AC: 4981 AN: 68020

Other (OTH) AF: 0.113 AC: 238 AN: 2112

Alfa AF: 0.0936 Hom.: 485

Bravo AF: 0.116

Asia WGS AF: 0.199 AC: 690 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	2.0
DANN	Benign	0.29
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs16929770; hg19: chr9-117275129;