chr9-16911759-G-A

Variant names:

• chr9-16911759-G-A
• rs4445329

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 0.411 in 151,758 control chromosomes in the GnomAD database, including 13,931 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 0.41 (13931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.411 AC: 62293 AN: 151640 Hom.: 13905 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.411 AC: 62371 AN: 151758 Hom.: 13931 Cov.: 31 AF XY: 0.412 AC XY: 30540 AN XY: 74172

African (AFR) AF: 0.549 AC: 22740 AN: 41388

American (AMR) AF: 0.532 AC: 8110 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1490 AN: 5134

South Asian (SAS) AF: 0.418 AC: 2014 AN: 4816

European-Finnish (FIN) AF: 0.288 AC: 3030 AN: 10504

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22133 AN: 67912

Other (OTH) AF: 0.415 AC: 872 AN: 2100

Alfa AF: 0.313 Hom.: 3112

Bravo AF: 0.434

Asia WGS AF: 0.408 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.17
DANN	Benign	0.61
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs4445329; hg19: chr9-16911757; COSMIC: COSV50775818;