rs10812428

Variant names:

• chr9-26614849-C-T
• rs10812428

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 0.398 in 151,980 control chromosomes in the GnomAD database, including 12,038 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 0.40 (12038 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 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: 0.398 AC: 60459 AN: 151862 Hom.: 12017 Cov.: 32

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.398 AC: 60526 AN: 151980 Hom.: 12038 Cov.: 32 AF XY: 0.399 AC XY: 29617 AN XY: 74284

African (AFR) AF: 0.440 AC: 18224 AN: 41446

American (AMR) AF: 0.419 AC: 6399 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3468

East Asian (EAS) AF: 0.363 AC: 1871 AN: 5152

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4814

European-Finnish (FIN) AF: 0.406 AC: 4282 AN: 10546

Middle Eastern (MID) AF: 0.329 AC: 96 AN: 292

European-Non Finnish (NFE) AF: 0.378 AC: 25715 AN: 67970

Other (OTH) AF: 0.401 AC: 845 AN: 2108

Alfa AF: 0.383 Hom.: 36627

Bravo AF: 0.402

Asia WGS AF: 0.327 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.4
DANN	Benign	0.90
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs10812428; hg19: chr9-26614847;