10-3820350-C-T

Position:

• chr10-3820350-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 0.454 in 152,062 control chromosomes in the GnomAD database, including 16,942 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 0.45 (16942 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.561 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: 0.454 AC: 69022 AN: 151944 Hom.: 16930 Cov.: 33

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.454 AC: 69060 AN: 152062 Hom.: 16942 Cov.: 33 AF XY: 0.450 AC XY: 33471 AN XY: 74354

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.566

Gnomad4 OTH AF: 0.460

Alfa AF: 0.536 Hom.: 49630

Bravo AF: 0.440

Asia WGS AF: 0.287 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.47
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6601764; hg19: chr10-3862542;