9-16914897-A-G

Variant names:

• chr9-16914897-A-G
• rs7032221

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 0.413 in 151,686 control chromosomes in the GnomAD database, including 14,012 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 (14012 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62507 AN: 151568 Hom.: 13987 Cov.: 30

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.413 AC: 62583 AN: 151686 Hom.: 14012 Cov.: 30 AF XY: 0.414 AC XY: 30666 AN XY: 74096

African (AFR) AF: 0.550 AC: 22740 AN: 41324

American (AMR) AF: 0.534 AC: 8129 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1441 AN: 5138

South Asian (SAS) AF: 0.417 AC: 2003 AN: 4800

European-Finnish (FIN) AF: 0.304 AC: 3198 AN: 10510

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

European-Non Finnish (NFE) AF: 0.327 AC: 22214 AN: 67912

Other (OTH) AF: 0.418 AC: 879 AN: 2104

Alfa AF: 0.414 Hom.: 2281

Bravo AF: 0.434

Asia WGS AF: 0.405 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.77
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7032221; hg19: chr9-16914895; COSMIC: COSV60335750;