rs379568

Positions:

• chr10-8083856-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.177 in 152,246 control chromosomes in the GnomAD database, including 3,295 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 0.18 (3295 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.59

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26854 AN: 152128 Hom.: 3273 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.177 AC: 26918 AN: 152246 Hom.: 3295 Cov.: 33 AF XY: 0.176 AC XY: 13072 AN XY: 74438

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.112

Gnomad4 SAS AF: 0.0843

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.160

Alfa AF: 0.119 Hom.: 1808

Bravo AF: 0.187

Asia WGS AF: 0.120 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	21
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs379568; hg19: chr10-8125819;