Genetic Variant :null (chr5-108706013-C-CT) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1BS2

The variant allele was found at a frequency of 0.00926 in 147,796 control chromosomes in the GnomAD database, including 8 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0093 ( 8 hom., cov: 22)

Consequence

Unknown

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

1 publications found

Variant links:

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ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00926 (1368/147796) while in subpopulation AFR AF = 0.0204 (828/40536). AF 95% confidence interval is 0.0193. There are 8 homozygotes in GnomAd4. There are 653 alleles in the male GnomAd4 subpopulation. Median coverage is 22. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 8 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:

0.00921

AC:

1360

AN:

147724

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0203

Gnomad AMI

AF:

0.00113

Gnomad AMR

AF:

0.00751

Gnomad ASJ

AF:

0.000879

Gnomad EAS

AF:

0.000197

Gnomad SAS

AF:

0.00108

Gnomad FIN

AF:

0.00588

Gnomad MID

AF:

0.00974

Gnomad NFE

AF:

0.00516

Gnomad OTH

AF:

0.00742

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

GnomAD4 genome

AF:

0.00926

AC:

1368

AN:

147796

Hom.:

Cov.:

AF XY:

0.00908

AC XY:

653

AN XY:

71948

show subpopulations

African (AFR)

AF:

0.0204

AC:

828

AN:

40536

American (AMR)

AF:

0.00751

AC:

111

AN:

14790

Ashkenazi Jewish (ASJ)

AF:

0.000879

AC:

AN:

3414

East Asian (EAS)

AF:

0.000197

AC:

AN:

5066

South Asian (SAS)

AF:

0.00108

AC:

AN:

4636

European-Finnish (FIN)

AF:

0.00588

AC:

AN:

9524

Middle Eastern (MID)

AF:

0.0141

AC:

AN:

284

European-Non Finnish (NFE)

AF:

0.00516

AC:

344

AN:

66618

Other (OTH)

AF:

0.00735

AC:

AN:

2040

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

125

187

250

312

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.000811

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.1

Splicing

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

Publications

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5-108706013-CTT-CTTT

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over