chr10-92661060-C-T

Variant names:

• chr10-92661060-C-T
• rs78216286

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.128 AC: 5282 AN: 41282

American (AMR) AF: 0.138 AC: 2102 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0327 AC: 113 AN: 3458

East Asian (EAS) AF: 0.118 AC: 602 AN: 5114

South Asian (SAS) AF: 0.118 AC: 567 AN: 4788

European-Finnish (FIN) AF: 0.0113 AC: 119 AN: 10534

Middle Eastern (MID) AF: 0.0377 AC: 11 AN: 292

European-Non Finnish (NFE) AF: 0.0307 AC: 2084 AN: 67860

Other (OTH) AF: 0.0661 AC: 139 AN: 2104

Alfa AF: 0.0547 Hom.: 64

Bravo AF: 0.0849

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		0.21

Splicing

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

Other links and lift over

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