rs9905480

Variant names:

• chr17-50858704-C-T
• rs9905480

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 0.294 in 151,908 control chromosomes in the GnomAD database, including 6,626 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 0.29 (6626 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.327 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: 0.294 AC: 44575 AN: 151790 Hom.: 6627 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.294 AC: 44605 AN: 151908 Hom.: 6626 Cov.: 31 AF XY: 0.289 AC XY: 21435 AN XY: 74222

African (AFR) AF: 0.245 AC: 10150 AN: 41410

American (AMR) AF: 0.250 AC: 3824 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3466

East Asian (EAS) AF: 0.283 AC: 1458 AN: 5154

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4822

European-Finnish (FIN) AF: 0.306 AC: 3226 AN: 10532

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22457 AN: 67948

Other (OTH) AF: 0.298 AC: 625 AN: 2098

Alfa AF: 0.315 Hom.: 32196

Bravo AF: 0.288

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.5
DANN	Benign	0.53
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs9905480; hg19: chr17-48936065;