rs9915822

Variant names:

• chr17-56589374-A-C
• rs9915822

Your query was ambiguous. Multiple possible variants found:

• chr17-56589374-A-C
• chr17-56589374-A-G

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 0.447 in 152,094 control chromosomes in the GnomAD database, including 15,709 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 (15709 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.834
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.447 AC: 68003 AN: 151976 Hom.: 15709 Cov.: 33

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.447 AC: 68022 AN: 152094 Hom.: 15709 Cov.: 33 AF XY: 0.452 AC XY: 33607 AN XY: 74330

African (AFR) AF: 0.358 AC: 14860 AN: 41490

American (AMR) AF: 0.530 AC: 8097 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3466

East Asian (EAS) AF: 0.681 AC: 3513 AN: 5158

South Asian (SAS) AF: 0.608 AC: 2932 AN: 4820

European-Finnish (FIN) AF: 0.396 AC: 4183 AN: 10568

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31012 AN: 67996

Other (OTH) AF: 0.495 AC: 1046 AN: 2114

Alfa AF: 0.463 Hom.: 61847

Bravo AF: 0.451

Asia WGS AF: 0.628 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.3
DANN	Benign	0.65
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs9915822; hg19: chr17-54666735;