chr10-46057646-A-G

Variant names:

• chr10-46057646-A-G
• rs11006207

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 0.455 in 152,088 control chromosomes in the GnomAD database, including 17,407 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 0.45 (17407 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69148 AN: 151972 Hom.: 17414 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.461

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

GnomAD4 genome AF: 0.455 AC: 69140 AN: 152088 Hom.: 17407 Cov.: 32 AF XY: 0.457 AC XY: 33942 AN XY: 74348

African (AFR) AF: 0.227 AC: 9426 AN: 41524

American (AMR) AF: 0.541 AC: 8254 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3464

East Asian (EAS) AF: 0.521 AC: 2686 AN: 5154

South Asian (SAS) AF: 0.412 AC: 1989 AN: 4826

European-Finnish (FIN) AF: 0.611 AC: 6462 AN: 10584

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37258 AN: 67968

Other (OTH) AF: 0.456 AC: 962 AN: 2110

Alfa AF: 0.507 Hom.: 13910

Bravo AF: 0.445

Asia WGS AF: 0.411 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.84
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs11006207; hg19: chr10-51538176;