rs684395

Variant names:

• chr10-30430183-C-G
• rs684395

Your query was ambiguous. Multiple possible variants found:

• chr10-30430183-C-G
• chr10-30430183-C-T

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 0.46 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.182 AC: 7530 AN: 41474

American (AMR) AF: 0.518 AC: 7899 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 1774 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1911 AN: 5160

South Asian (SAS) AF: 0.331 AC: 1593 AN: 4818

European-Finnish (FIN) AF: 0.601 AC: 6345 AN: 10560

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41152 AN: 67940

Other (OTH) AF: 0.481 AC: 1015 AN: 2108

Alfa AF: 0.537 Hom.: 2970

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
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs684395; hg19: chr10-30719112;