rs16936474

Variant names:

• chr9-113377555-G-A
• rs16936474

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 0.184 in 151,706 control chromosomes in the GnomAD database, including 3,058 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 0.18 (3058 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.221
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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: 0.184 AC: 27919 AN: 151592 Hom.: 3049 Cov.: 30

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0993

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.184 AC: 27961 AN: 151706 Hom.: 3058 Cov.: 30 AF XY: 0.182 AC XY: 13455 AN XY: 74124

African (AFR) AF: 0.289 AC: 11963 AN: 41338

American (AMR) AF: 0.142 AC: 2174 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 530 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1592 AN: 5058

South Asian (SAS) AF: 0.145 AC: 695 AN: 4798

European-Finnish (FIN) AF: 0.0993 AC: 1049 AN: 10564

Middle Eastern (MID) AF: 0.144 AC: 42 AN: 292

European-Non Finnish (NFE) AF: 0.140 AC: 9477 AN: 67912

Other (OTH) AF: 0.175 AC: 369 AN: 2104

Alfa AF: 0.155 Hom.: 8553

Bravo AF: 0.191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.3
DANN	Benign	0.62
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs16936474; hg19: chr9-116139835;