19-39245644-C-CATATATATATAT

Variant names:

• chr19-39245644-C-CATATATATATAT
• rs67461793

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

It is difficult to determine the true allele frequency of this variant because it is of type INS_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 0.00063 (0 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 1 publications found

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

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: 0.000633 AC: 87 AN: 137518 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000995

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000150

Gnomad ASJ AF: 0.000897

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.000242

Gnomad FIN AF: 0.000131

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000436

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.000632 AC: 87 AN: 137568 Hom.: 0 Cov.: 0 AF XY: 0.000530 AC XY: 35 AN XY: 66014

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000993 AC: 37 AN: 37262

American (AMR) AF: 0.000150 AC: 2 AN: 13340

Ashkenazi Jewish (ASJ) AF: 0.000897 AC: 3 AN: 3344

East Asian (EAS) AF: 0.00329 AC: 15 AN: 4562

South Asian (SAS) AF: 0.000243 AC: 1 AN: 4112

European-Finnish (FIN) AF: 0.000131 AC: 1 AN: 7658

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 270

European-Non Finnish (NFE) AF: 0.000436 AC: 28 AN: 64252

Other (OTH) AF: 0.00 AC: 0 AN: 1908

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.24

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: rs67461793; hg19: chr19-39736284;