rs684395

chr10-30430183-C-G

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 0.46 in 151,986 control chromosomes in the GnomAD database, including 18,749 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 0.46 (18749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 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: 0.460 AC: 69874 AN: 151868 Hom.: 18757 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.511

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.460 AC: 69882 AN: 151986 Hom.: 18749 Cov.: 32 AF XY: 0.458 AC XY: 33996 AN XY: 74292

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.511

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.481

Alfa AF: 0.503 Hom.: 1974

Bravo AF: 0.441

Asia WGS AF: 0.347 AC: 1206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.41
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs684395; hg19: chr10-30719112;