rs533343

Variant names:

• chr10-95574736-G-A
• rs533343

Your query was ambiguous. Multiple possible variants found:

• chr10-95574736-G-A
• chr10-95574736-G-T

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 0.627 in 151,914 control chromosomes in the GnomAD database, including 30,740 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 0.63 (30740 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.628 AC: 95296 AN: 151796 Hom.: 30747 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.627 AC: 95310 AN: 151914 Hom.: 30740 Cov.: 31 AF XY: 0.624 AC XY: 46349 AN XY: 74236

African (AFR) AF: 0.480 AC: 19863 AN: 41360

American (AMR) AF: 0.681 AC: 10400 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2127 AN: 3468

East Asian (EAS) AF: 0.681 AC: 3511 AN: 5154

South Asian (SAS) AF: 0.460 AC: 2214 AN: 4810

European-Finnish (FIN) AF: 0.703 AC: 7415 AN: 10554

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47765 AN: 67978

Other (OTH) AF: 0.610 AC: 1290 AN: 2114

Alfa AF: 0.674 Hom.: 12179

Bravo AF: 0.626

Asia WGS AF: 0.563 AC: 1958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs533343; hg19: chr10-97334493;