rs10858396

Variant names:

• chr9-135383930-G-A
• rs10858396

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 0.285 in 152,076 control chromosomes in the GnomAD database, including 6,883 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 0.28 (6883 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 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: 0.285 AC: 43278 AN: 151958 Hom.: 6864 Cov.: 33

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.285 AC: 43336 AN: 152076 Hom.: 6883 Cov.: 33 AF XY: 0.282 AC XY: 20974 AN XY: 74344

Gnomad4 AFR AF: 0.426

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.250

Alfa AF: 0.231 Hom.: 6384

Bravo AF: 0.301

Asia WGS AF: 0.154 AC: 536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10858396; hg19: chr9-138275776;