rs10114408

Variant names:

• chr9-93868852-A-T
• rs10114408

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 0.349 in 151,702 control chromosomes in the GnomAD database, including 9,481 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 0.35 (9481 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.365 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: 0.349 AC: 52924 AN: 151584 Hom.: 9479 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.349 AC: 52959 AN: 151702 Hom.: 9481 Cov.: 32 AF XY: 0.342 AC XY: 25348 AN XY: 74138

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.444

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.381

Alfa AF: 0.352 Hom.: 1190

Bravo AF: 0.353

Asia WGS AF: 0.292 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10114408; hg19: chr9-96631134;