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:

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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

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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