10-73949409-TTTTATTTATTTATTTATTTATTTATTTA-TTTTATTTATTTATTTA

Variant names:

• chr10-73949409-TTTTATTTATTTA-T
• rs3998225

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

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 0.12 (1100 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.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

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: 0.120 AC: 16202 AN: 134808 Hom.: 1098 Cov.: 0

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0168

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0527

Gnomad SAS AF: 0.0634

Gnomad FIN AF: 0.0565

Gnomad MID AF: 0.100

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.120 AC: 16215 AN: 134844 Hom.: 1100 Cov.: 0 AF XY: 0.117 AC XY: 7586 AN XY: 64568

African (AFR) AF: 0.179 AC: 6453 AN: 36082

American (AMR) AF: 0.110 AC: 1434 AN: 13064

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 527 AN: 3312

East Asian (EAS) AF: 0.0526 AC: 241 AN: 4578

South Asian (SAS) AF: 0.0642 AC: 261 AN: 4066

European-Finnish (FIN) AF: 0.0565 AC: 400 AN: 7080

Middle Eastern (MID) AF: 0.106 AC: 29 AN: 274

European-Non Finnish (NFE) AF: 0.104 AC: 6603 AN: 63784

Other (OTH) AF: 0.143 AC: 253 AN: 1770

Alfa AF: 0.0722 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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3998225;

hg19: chr10-75709167;