rs10961684

chr9-14728054-C-T

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 0.298 in 152,018 control chromosomes in the GnomAD database, including 7,616 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 0.30 (7616 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45135 AN: 151900 Hom.: 7583 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.298 AC: 45228 AN: 152018 Hom.: 7616 Cov.: 32 AF XY: 0.294 AC XY: 21811 AN XY: 74298

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.284

Alfa AF: 0.273 Hom.: 1719

Bravo AF: 0.303

Asia WGS AF: 0.205 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.9
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10961684; hg19: chr9-14728052;