10-52776102-A-G

Variant names:

• chr10-52776102-A-G
• rs2384045

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 0.637 in 151,938 control chromosomes in the GnomAD database, including 30,993 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 0.64 (30993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.723 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: 0.637 AC: 96708 AN: 151820 Hom.: 30967 Cov.: 32

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.644

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.589

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.637 AC: 96791 AN: 151938 Hom.: 30993 Cov.: 32 AF XY: 0.637 AC XY: 47309 AN XY: 74264

African (AFR) AF: 0.730 AC: 30261 AN: 41462

American (AMR) AF: 0.649 AC: 9908 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.644 AC: 2235 AN: 3470

East Asian (EAS) AF: 0.660 AC: 3398 AN: 5148

South Asian (SAS) AF: 0.587 AC: 2827 AN: 4818

European-Finnish (FIN) AF: 0.578 AC: 6098 AN: 10552

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.589 AC: 40011 AN: 67922

Other (OTH) AF: 0.613 AC: 1292 AN: 2108

Alfa AF: 0.615 Hom.: 6538

Bravo AF: 0.650

Asia WGS AF: 0.640 AC: 2225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.30
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2384045; hg19: chr10-54535862;