rs16933006

Variant names:

• chr9-15335916-A-C
• rs16933006

Your query was ambiguous. Multiple possible variants found:

• chr9-15335916-A-C
• chr9-15335916-A-G

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 0.139 in 152,146 control chromosomes in the GnomAD database, including 1,761 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 0.14 (1761 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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: 0.139 AC: 21168 AN: 152028 Hom.: 1758 Cov.: 33

Gnomad AFR AF: 0.0884

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.139 AC: 21181 AN: 152146 Hom.: 1761 Cov.: 33 AF XY: 0.147 AC XY: 10899 AN XY: 74368

African (AFR) AF: 0.0883 AC: 3669 AN: 41544

American (AMR) AF: 0.105 AC: 1609 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 626 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1595 AN: 5160

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4820

European-Finnish (FIN) AF: 0.221 AC: 2333 AN: 10550

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9759 AN: 67996

Other (OTH) AF: 0.137 AC: 290 AN: 2116

Alfa AF: 0.128 Hom.: 2327

Bravo AF: 0.127

Asia WGS AF: 0.246 AC: 858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.0
DANN	Benign	0.82
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs16933006; hg19: chr9-15335914; COSMIC: COSV69449677;