rs10964899

Positions:

• chr9-21188353-T-C
• chr9-21188353-T-G

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 0.224 in 152,110 control chromosomes in the GnomAD database, including 4,258 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 0.22 (4258 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.224 AC: 33972 AN: 151992 Hom.: 4246 Cov.: 33

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.224 AC: 34036 AN: 152110 Hom.: 4258 Cov.: 33 AF XY: 0.224 AC XY: 16686 AN XY: 74354

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.216

Alfa AF: 0.207 Hom.: 423

Bravo AF: 0.234

Asia WGS AF: 0.256 AC: 892 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.83
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10964899; hg19: chr9-21188352;