rs10818069

Variant names:

• chr9-117691693-C-A
• rs10818069

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 0.0582 in 152,058 control chromosomes in the GnomAD database, including 320 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 0.058 (320 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 6 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 (SAS) allele frequency at 95% confidence interval = 0.111 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: 0.0583 AC: 8860 AN: 151940 Hom.: 321 Cov.: 32

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0501

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0756

Gnomad OTH AF: 0.0557

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

GnomAD4 genome AF: 0.0582 AC: 8856 AN: 152058 Hom.: 320 Cov.: 32 AF XY: 0.0604 AC XY: 4487 AN XY: 74328

African (AFR) AF: 0.0230 AC: 957 AN: 41546

American (AMR) AF: 0.0500 AC: 764 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3466

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5162

South Asian (SAS) AF: 0.119 AC: 575 AN: 4824

European-Finnish (FIN) AF: 0.101 AC: 1069 AN: 10590

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0756 AC: 5134 AN: 67890

Other (OTH) AF: 0.0546 AC: 115 AN: 2106

Alfa AF: 0.0645 Hom.: 48

Bravo AF: 0.0499

Asia WGS AF: 0.0660 AC: 228 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	0.50
DANN	Benign	0.59
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10818069; hg19: chr9-120453971;