rs9905973

Variant names:

• chr17-28408124-G-A
• rs9905973

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 0.325 in 152,026 control chromosomes in the GnomAD database, including 8,525 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 0.33 (8525 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 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: 0.325 AC: 49387 AN: 151908 Hom.: 8515 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.325 AC: 49428 AN: 152026 Hom.: 8525 Cov.: 32 AF XY: 0.324 AC XY: 24111 AN XY: 74318

African (AFR) AF: 0.431 AC: 17858 AN: 41432

American (AMR) AF: 0.371 AC: 5675 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1447 AN: 5172

South Asian (SAS) AF: 0.281 AC: 1354 AN: 4820

European-Finnish (FIN) AF: 0.229 AC: 2416 AN: 10572

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.274 AC: 18651 AN: 67972

Other (OTH) AF: 0.330 AC: 696 AN: 2110

Alfa AF: 0.301 Hom.: 1557

Bravo AF: 0.339

Asia WGS AF: 0.252 AC: 877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs9905973; hg19: chr17-26735142;