rs9901146

Variant names:

• chr17-39887090-G-A
• rs9901146

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 0.452 in 151,926 control chromosomes in the GnomAD database, including 15,811 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 0.45 (15811 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.452 AC: 68609 AN: 151806 Hom.: 15792 Cov.: 31

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.452 AC: 68676 AN: 151926 Hom.: 15811 Cov.: 31 AF XY: 0.453 AC XY: 33654 AN XY: 74252

African (AFR) AF: 0.392 AC: 16238 AN: 41432

American (AMR) AF: 0.423 AC: 6454 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3470

East Asian (EAS) AF: 0.270 AC: 1397 AN: 5168

South Asian (SAS) AF: 0.389 AC: 1874 AN: 4816

European-Finnish (FIN) AF: 0.575 AC: 6048 AN: 10526

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.493 AC: 33523 AN: 67948

Other (OTH) AF: 0.433 AC: 914 AN: 2112

Alfa AF: 0.440 Hom.: 3946

Bravo AF: 0.430

Asia WGS AF: 0.396 AC: 1376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.47
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs9901146; hg19: chr17-38043343;