rs10511869

Variant names:

• chr9-30899972-G-A
• rs10511869

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 0.0483 in 152,012 control chromosomes in the GnomAD database, including 446 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 0.048 (446 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.874

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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: 0.0480 AC: 7298 AN: 151894 Hom.: 437 Cov.: 32

Gnomad AFR AF: 0.0771

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00872

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0483 AC: 7340 AN: 152012 Hom.: 446 Cov.: 32 AF XY: 0.0522 AC XY: 3875 AN XY: 74276

Gnomad4 AFR AF: 0.0780

Gnomad4 AMR AF: 0.0552

Gnomad4 ASJ AF: 0.0164

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.0294

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.00873

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0390 Hom.: 46

Bravo AF: 0.0527

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.93
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511869; hg19: chr9-30899970;