10-33547113-A-G

Variant names:

• chr10-33547113-A-G
• rs1869237

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.406 in 152,004 control chromosomes in the GnomAD database, including 14,509 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 (14509 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.32

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 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: 0.406 AC: 61713 AN: 151886 Hom.: 14503 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.406 AC: 61723 AN: 152004 Hom.: 14509 Cov.: 32 AF XY: 0.418 AC XY: 31082 AN XY: 74278

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.405

Alfa AF: 0.414 Hom.: 22055

Bravo AF: 0.402

Asia WGS AF: 0.795 AC: 2751 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	19
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1869237; hg19: chr10-33836041;