rs10105543

Variant names:

• chr8-9466005-C-T
• rs10105543

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 0.327 in 151,918 control chromosomes in the GnomAD database, including 8,344 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 0.33 (8344 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 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: 0.327 AC: 49583 AN: 151800 Hom.: 8331 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.327 AC: 49641 AN: 151918 Hom.: 8344 Cov.: 32 AF XY: 0.327 AC XY: 24281 AN XY: 74244

African (AFR) AF: 0.375 AC: 15537 AN: 41386

American (AMR) AF: 0.288 AC: 4399 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3466

East Asian (EAS) AF: 0.168 AC: 868 AN: 5170

South Asian (SAS) AF: 0.368 AC: 1770 AN: 4812

European-Finnish (FIN) AF: 0.305 AC: 3216 AN: 10540

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21645 AN: 67974

Other (OTH) AF: 0.330 AC: 697 AN: 2110

Alfa AF: 0.326 Hom.: 13829

Bravo AF: 0.330

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.68
DANN	Benign	0.77
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs10105543; hg19: chr8-9323515;