10-20573472-C-T

Position:

• chr10-20573472-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 0.0385 in 152,224 control chromosomes in the GnomAD database, including 131 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 0.038 (131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.875

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 (AFR) allele frequency at 95% confidence interval = 0.0644 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: 0.0385 AC: 5849 AN: 152106 Hom.: 130 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0269

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0112

Gnomad FIN AF: 0.0428

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0301

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0385 AC: 5855 AN: 152224 Hom.: 131 Cov.: 32 AF XY: 0.0380 AC XY: 2828 AN XY: 74430

Gnomad4 AFR AF: 0.0665

Gnomad4 AMR AF: 0.0269

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0110

Gnomad4 FIN AF: 0.0428

Gnomad4 NFE AF: 0.0301

Gnomad4 OTH AF: 0.0307

Alfa AF: 0.0195 Hom.: 7

Bravo AF: 0.0381

Asia WGS AF: 0.0130 AC: 46 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	9.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11012167; hg19: chr10-20862401;