10-58316293-T-G

Position:

• chr10-58316293-T-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 0.0403 in 152,188 control chromosomes in the GnomAD database, including 232 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 0.040 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.526

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0956 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: 0.0402 AC: 6119 AN: 152070 Hom.: 231 Cov.: 32

Gnomad AFR AF: 0.0980

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.00188

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0403 AC: 6132 AN: 152188 Hom.: 232 Cov.: 32 AF XY: 0.0404 AC XY: 3003 AN XY: 74420

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.0213

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0494

Gnomad4 FIN AF: 0.00188

Gnomad4 NFE AF: 0.0185

Gnomad4 OTH AF: 0.0351

Alfa AF: 0.0329 Hom.: 30

Bravo AF: 0.0429

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2486489; hg19: chr10-60076053;