10-92706670-T-C

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 0.428 in 151,814 control chromosomes in the GnomAD database, including 14,526 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 0.43 (14526 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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: 0.428 AC: 64976 AN: 151698 Hom.: 14529 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.428 AC: 65007 AN: 151814 Hom.: 14526 Cov.: 31 AF XY: 0.433 AC XY: 32120 AN XY: 74162

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.824

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.419

Alfa AF: 0.419 Hom.: 1693

Bravo AF: 0.429

Asia WGS AF: 0.621 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.32
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11187139; hg19: chr10-94466427;