rs533383

Variant names:

• chr10-95574722-C-T
• rs533383

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 0.482 in 151,910 control chromosomes in the GnomAD database, including 20,828 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 0.48 (20828 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.437
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73188 AN: 151792 Hom.: 20830 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.596

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.482 AC: 73190 AN: 151910 Hom.: 20828 Cov.: 31 AF XY: 0.483 AC XY: 35835 AN XY: 74238

African (AFR) AF: 0.160 AC: 6606 AN: 41406

American (AMR) AF: 0.584 AC: 8901 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.472 AC: 1637 AN: 3468

East Asian (EAS) AF: 0.595 AC: 3072 AN: 5160

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4812

European-Finnish (FIN) AF: 0.649 AC: 6830 AN: 10528

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42527 AN: 67968

Other (OTH) AF: 0.473 AC: 1001 AN: 2116

Alfa AF: 0.566 Hom.: 65944

Bravo AF: 0.467

Asia WGS AF: 0.474 AC: 1649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs533383; hg19: chr10-97334479;