rs817826

Variant names:

• chr9-107394019-C-T
• rs817826

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 0.811 in 152,142 control chromosomes in the GnomAD database, including 50,407 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 0.81 (50407 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 49 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 (EAS) allele frequency at 95% confidence interval = 0.878 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: 0.811 AC: 123321 AN: 152024 Hom.: 50369 Cov.: 33

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.811 AC: 123410 AN: 152142 Hom.: 50407 Cov.: 33 AF XY: 0.813 AC XY: 60512 AN XY: 74396

African (AFR) AF: 0.705 AC: 29223 AN: 41466

American (AMR) AF: 0.847 AC: 12962 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2701 AN: 3472

East Asian (EAS) AF: 0.900 AC: 4644 AN: 5162

South Asian (SAS) AF: 0.795 AC: 3836 AN: 4824

European-Finnish (FIN) AF: 0.859 AC: 9108 AN: 10606

Middle Eastern (MID) AF: 0.830 AC: 244 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58115 AN: 68000

Other (OTH) AF: 0.820 AC: 1726 AN: 2106

Alfa AF: 0.843 Hom.: 230652

Bravo AF: 0.809

Asia WGS AF: 0.842 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.64
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs817826; hg19: chr9-110156300;