10-123229073-A-G

Variant names:

• chr10-123229073-A-G
• rs766295

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 0.193 in 152,160 control chromosomes in the GnomAD database, including 3,152 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 0.19 (3152 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.241 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: 0.194 AC: 29444 AN: 152042 Hom.: 3154 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0643

Gnomad SAS AF: 0.0813

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.193 AC: 29437 AN: 152160 Hom.: 3152 Cov.: 32 AF XY: 0.187 AC XY: 13915 AN XY: 74404

African (AFR) AF: 0.143 AC: 5943 AN: 41490

American (AMR) AF: 0.158 AC: 2413 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3470

East Asian (EAS) AF: 0.0640 AC: 332 AN: 5186

South Asian (SAS) AF: 0.0812 AC: 392 AN: 4830

European-Finnish (FIN) AF: 0.207 AC: 2192 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16612 AN: 67984

Other (OTH) AF: 0.197 AC: 416 AN: 2110

Alfa AF: 0.223 Hom.: 17037

Bravo AF: 0.190

Asia WGS AF: 0.0780 AC: 270 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.19
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs766295; hg19: chr10-124988589;