10-73949409-TTTTATTTATTTATTTATTTATTTATTTA-TTTTATTTATTTA

Variant names:

• chr10-73949409-TTTTATTTATTTATTTA-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 0.011 (29 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 afr. GnomAd4 allele frequency = 0.0111 (1501/134946) while in subpopulation AFR AF = 0.0368 (1330/36122). AF 95% confidence interval is 0.0352. There are 29 homozygotes in GnomAd4. There are 737 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 29 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: 0.0111 AC: 1493 AN: 134908 Hom.: 29 Cov.: 0

Gnomad AFR AF: 0.0367

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00482

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00196

Gnomad SAS AF: 0.00220

Gnomad FIN AF: 0.000705

Gnomad MID AF: 0.00333

Gnomad NFE AF: 0.00105

Gnomad OTH AF: 0.00970

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

GnomAD4 genome AF: 0.0111 AC: 1501 AN: 134946 Hom.: 29 Cov.: 0 AF XY: 0.0114 AC XY: 737 AN XY: 64620

African (AFR) AF: 0.0368 AC: 1330 AN: 36122

American (AMR) AF: 0.00482 AC: 63 AN: 13074

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3316

East Asian (EAS) AF: 0.00197 AC: 9 AN: 4578

South Asian (SAS) AF: 0.00221 AC: 9 AN: 4070

European-Finnish (FIN) AF: 0.000705 AC: 5 AN: 7090

Middle Eastern (MID) AF: 0.00365 AC: 1 AN: 274

European-Non Finnish (NFE) AF: 0.00105 AC: 67 AN: 63818

Other (OTH) AF: 0.00960 AC: 17 AN: 1770

Alfa AF: 0.000647 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;