rs508384

chr10-100365004-C-Achr10-100365004-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 0.243 in 151,880 control chromosomes in the GnomAD database, including 5,353 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 0.24 (5353 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.39 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: 0.242 AC: 36761 AN: 151762 Hom.: 5317 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.243 AC: 36839 AN: 151880 Hom.: 5353 Cov.: 31 AF XY: 0.243 AC XY: 18035 AN XY: 74240

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.214

Alfa AF: 0.172 Hom.: 2494

Bravo AF: 0.244

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	7.4
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: rs508384; hg19: chr10-102124761;