rs16931058

Variant names:

• chr9-114705273-G-A
• rs16931058

Your query was ambiguous. Multiple possible variants found:

• chr9-114705273-G-A
• chr9-114705273-G-T

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 0.118 in 151,628 control chromosomes in the GnomAD database, including 1,648 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 0.12 (1648 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 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: 0.118 AC: 17883 AN: 151528 Hom.: 1650 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.0682

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0412

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.118 AC: 17898 AN: 151628 Hom.: 1648 Cov.: 31 AF XY: 0.126 AC XY: 9355 AN XY: 74044

African (AFR) AF: 0.186 AC: 7693 AN: 41276

American (AMR) AF: 0.203 AC: 3102 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0682 AC: 236 AN: 3460

East Asian (EAS) AF: 0.308 AC: 1585 AN: 5148

South Asian (SAS) AF: 0.130 AC: 624 AN: 4788

European-Finnish (FIN) AF: 0.139 AC: 1450 AN: 10442

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.0412 AC: 2801 AN: 67972

Other (OTH) AF: 0.108 AC: 227 AN: 2098

Alfa AF: 0.107 Hom.: 268

Bravo AF: 0.134

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.37
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs16931058; hg19: chr9-117467553;