10-92677094-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 0.529 in 151,278 control chromosomes in the GnomAD database, including 21,471 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 0.53 (21471 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 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: 0.529 AC: 79964 AN: 151160 Hom.: 21459 Cov.: 29

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.529 AC: 80016 AN: 151278 Hom.: 21471 Cov.: 29 AF XY: 0.527 AC XY: 38893 AN XY: 73824

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.513

Alfa AF: 0.519 Hom.: 3589

Bravo AF: 0.526

Asia WGS AF: 0.622 AC: 2163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	12
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7911264; hg19: chr10-94436851;