10-30381762-C-T

Position:

• chr10-30381762-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 0.74 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.771

Alfa AF: 0.769 Hom.: 21423

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2480285; hg19: chr10-30670691;