10-46054955-A-G

Position:

• chr10-46054955-A-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 0.454 in 151,460 control chromosomes in the GnomAD database, including 17,243 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 (17243 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 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: 68786 AN: 151348 Hom.: 17250 Cov.: 30

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.454 AC: 68778 AN: 151460 Hom.: 17243 Cov.: 30 AF XY: 0.456 AC XY: 33693 AN XY: 73942

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.457

Alfa AF: 0.510 Hom.: 2612

Bravo AF: 0.445

Asia WGS AF: 0.409 AC: 1423 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4630243; hg19: chr10-51540867;