10-92661060-C-T

Position:

• chr10-92661060-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 0.0727 in 151,574 control chromosomes in the GnomAD database, including 636 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 0.073 (636 hom., cov: 31)
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.133 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: 0.0725 AC: 10984 AN: 151454 Hom.: 635 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0327

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0318

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0639

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

GnomAD4 genome AF: 0.0727 AC: 11019 AN: 151574 Hom.: 636 Cov.: 31 AF XY: 0.0748 AC XY: 5542 AN XY: 74052

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.0327

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.0113

Gnomad4 NFE AF: 0.0307

Gnomad4 OTH AF: 0.0661

Alfa AF: 0.0521 Hom.: 61

Bravo AF: 0.0849

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78216286; hg19: chr10-94420817; COSMIC: COSV73845825;