10-132482311-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 0.123 in 152,154 control chromosomes in the GnomAD database, including 2,833 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 0.12 (2833 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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 = 0.359 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: 0.123 AC: 18725 AN: 152036 Hom.: 2817 Cov.: 33

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.00452

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0213

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.123 AC: 18775 AN: 152154 Hom.: 2833 Cov.: 33 AF XY: 0.119 AC XY: 8866 AN XY: 74404

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.0711

Gnomad4 ASJ AF: 0.0530

Gnomad4 EAS AF: 0.0589

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.00452

Gnomad4 NFE AF: 0.0213

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0662 Hom.: 210

Bravo AF: 0.138

Asia WGS AF: 0.0780 AC: 273 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	5.2
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73389468; hg19: chr10-134295815;