rs757099

Variant names:

• chr9-25737569-T-C
• rs757099

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 0.386 in 152,076 control chromosomes in the GnomAD database, including 12,088 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 0.39 (12088 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 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: 0.387 AC: 58739 AN: 151958 Hom.: 12096 Cov.: 33

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.477

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.386 AC: 58733 AN: 152076 Hom.: 12088 Cov.: 33 AF XY: 0.387 AC XY: 28786 AN XY: 74350

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.503

Gnomad4 FIN AF: 0.394

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.418

Alfa AF: 0.446 Hom.: 30250

Bravo AF: 0.376

Asia WGS AF: 0.394 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs757099; hg19: chr9-25737567;