Genetic Variant :null (chr19-39245644-C-CATATATAT) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0033 ( 2 hom., cov: 0)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

1 publications found

Variant links:

Genome browser will be placed here

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.00336

AC:

462

AN:

137564

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00562

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00120

Gnomad ASJ

AF:

0.00149

Gnomad EAS

AF:

0.00721

Gnomad SAS

AF:

0.00338

Gnomad FIN

AF:

0.00131

Gnomad MID

AF:

0.00676

Gnomad NFE

AF:

0.00264

Gnomad OTH

AF:

0.00158

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

GnomAD4 genome

AF:

0.00335

AC:

461

AN:

137616

Hom.:

Cov.:

AF XY:

0.00306

AC XY:

202

AN XY:

66032

show subpopulations

African (AFR)

AF:

0.00564

AC:

210

AN:

37258

American (AMR)

AF:

0.00120

AC:

AN:

13348

Ashkenazi Jewish (ASJ)

AF:

0.00149

AC:

AN:

3346

East Asian (EAS)

AF:

0.00701

AC:

AN:

4562

South Asian (SAS)

AF:

0.00340

AC:

AN:

4116

European-Finnish (FIN)

AF:

0.00131

AC:

AN:

7660

Middle Eastern (MID)

AF:

0.00370

AC:

AN:

270

European-Non Finnish (NFE)

AF:

0.00264

AC:

170

AN:

64288

Other (OTH)

AF:

0.00157

AC:

AN:

1908

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

677

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.24

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

19-39245644-CATATATATATATATATAT-CATATATATATATATATATATATATAT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over