rs9633774

chr10-10053380-G-A

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 0.407 in 152,150 control chromosomes in the GnomAD database, including 12,875 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 0.41 (12875 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61912 AN: 152032 Hom.: 12859 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.407 AC: 61965 AN: 152150 Hom.: 12875 Cov.: 33 AF XY: 0.413 AC XY: 30695 AN XY: 74384

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.414

Alfa AF: 0.404 Hom.: 5861

Bravo AF: 0.391

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9633774; hg19: chr10-10095343;