10-73949409-TTTTATTTATTTATTTATTTATTTATTTA-TTTTA

Variant names:

• chr10-73949409-TTTTATTTATTTATTTATTTATTTA-T
• rs3998225

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.012 (13 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.639
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0124 (1680/134966) while in subpopulation NFE AF = 0.0201 (1283/63820). AF 95% confidence interval is 0.0192. There are 13 homozygotes in GnomAd4. There are 778 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 13 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0124 AC: 1679 AN: 134928 Hom.: 13 Cov.: 0

Gnomad AFR AF: 0.00338

Gnomad AMI AF: 0.0144

Gnomad AMR AF: 0.00567

Gnomad ASJ AF: 0.00905

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0105

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0300

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0188

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

GnomAD4 genome AF: 0.0124 AC: 1680 AN: 134966 Hom.: 13 Cov.: 0 AF XY: 0.0120 AC XY: 778 AN XY: 64630

African (AFR) AF: 0.00338 AC: 122 AN: 36136

American (AMR) AF: 0.00566 AC: 74 AN: 13076

Ashkenazi Jewish (ASJ) AF: 0.00905 AC: 30 AN: 3316

East Asian (EAS) AF: 0.00 AC: 0 AN: 4578

South Asian (SAS) AF: 0.0108 AC: 44 AN: 4070

European-Finnish (FIN) AF: 0.0103 AC: 73 AN: 7092

Middle Eastern (MID) AF: 0.0328 AC: 9 AN: 274

European-Non Finnish (NFE) AF: 0.0201 AC: 1283 AN: 63820

Other (OTH) AF: 0.0186 AC: 33 AN: 1770

Alfa AF: 0.0172 Hom.: 738

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs3998225; hg19: chr10-75709167;