rs10858396

Variant names:

• chr9-135383930-G-A
• rs10858396

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 0.285 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.426 AC: 17666 AN: 41458

American (AMR) AF: 0.318 AC: 4858 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 620 AN: 3472

East Asian (EAS) AF: 0.104 AC: 538 AN: 5164

South Asian (SAS) AF: 0.191 AC: 919 AN: 4820

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10590

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15814 AN: 67970

Other (OTH) AF: 0.250 AC: 527 AN: 2108

Alfa AF: 0.243 Hom.: 16332

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
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10858396; hg19: chr9-138275776;