chr10-30381762-C-T

Variant names:

• chr10-30381762-C-T
• rs2480285

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 0.74 in 152,024 control chromosomes in the GnomAD database, including 42,257 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 0.74 (42257 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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: 0.740 AC: 112451 AN: 151906 Hom.: 42226 Cov.: 31

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.740 AC: 112521 AN: 152024 Hom.: 42257 Cov.: 31 AF XY: 0.740 AC XY: 55005 AN XY: 74312

African (AFR) AF: 0.603 AC: 24948 AN: 41404

American (AMR) AF: 0.795 AC: 12133 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2742 AN: 3470

East Asian (EAS) AF: 0.825 AC: 4269 AN: 5172

South Asian (SAS) AF: 0.714 AC: 3441 AN: 4822

European-Finnish (FIN) AF: 0.798 AC: 8431 AN: 10570

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53935 AN: 67998

Other (OTH) AF: 0.771 AC: 1629 AN: 2114

Alfa AF: 0.767 Hom.: 21564

Bravo AF: 0.737

Asia WGS AF: 0.759 AC: 2637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.7
DANN	Benign	0.84
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2480285; hg19: chr10-30670691;