chr10-23402678-G-A

Variant names:

• chr10-23402678-G-A
• rs11013452

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 0.106 in 152,216 control chromosomes in the GnomAD database, including 1,580 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 0.11 (1580 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 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: 0.106 AC: 16183 AN: 152098 Hom.: 1578 Cov.: 30

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0541

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0444

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.106 AC: 16203 AN: 152216 Hom.: 1580 Cov.: 30 AF XY: 0.109 AC XY: 8097 AN XY: 74424

African (AFR) AF: 0.175 AC: 7270 AN: 41518

American (AMR) AF: 0.0951 AC: 1454 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3470

East Asian (EAS) AF: 0.511 AC: 2641 AN: 5166

South Asian (SAS) AF: 0.159 AC: 769 AN: 4824

European-Finnish (FIN) AF: 0.0541 AC: 574 AN: 10610

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3025 AN: 68026

Other (OTH) AF: 0.103 AC: 218 AN: 2112

Alfa AF: 0.0633 Hom.: 214

Bravo AF: 0.115

Asia WGS AF: 0.272 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.43
DANN	Benign	0.84
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs11013452; hg19: chr10-23691607;