rs575107

Variant names:

• chr9-110821628-G-A
• rs575107

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.106 in 152,206 control chromosomes in the GnomAD database, including 1,244 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 0.11 (1244 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 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: 0.106 AC: 16183 AN: 152088 Hom.: 1245 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.0399

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.106 AC: 16197 AN: 152206 Hom.: 1244 Cov.: 33 AF XY: 0.104 AC XY: 7767 AN XY: 74420

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.0699

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.0191

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0399

Gnomad4 NFE AF: 0.0697

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0811 Hom.: 380

Bravo AF: 0.112

Asia WGS AF: 0.0610 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.1
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs575107; hg19: chr9-113583908;