rs10105543

chr8-9466005-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.330

Alfa AF: 0.326 Hom.: 10967

Bravo AF: 0.330

Asia WGS AF: 0.273 AC: 951 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.68
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10105543; hg19: chr8-9323515;