10-92661060-C-T

Variant names:

• chr10-92661060-C-T
• rs78216286

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;