rs10114408

Variant names:

• chr9-93868852-A-T
• rs10114408

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.365 AC: 15100 AN: 41316

American (AMR) AF: 0.311 AC: 4748 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1537 AN: 3460

East Asian (EAS) AF: 0.205 AC: 1058 AN: 5162

South Asian (SAS) AF: 0.252 AC: 1214 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2961 AN: 10534

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25046 AN: 67836

Other (OTH) AF: 0.381 AC: 802 AN: 2106

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs10114408; hg19: chr9-96631134;