Genetic Variant :null (chr10-128610590-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.279 in 152,216 control chromosomes in the GnomAD database, including 6,275 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 6275 hom., cov: 34)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.366

Publications

1 publications found

Variant links:

COSMIC-nc: COSV63766147

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ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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:

0.279

AC:

42451

AN:

152098

Hom.:

6259

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.212

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.286

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.263

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

GnomAD4 genome

AF:

0.279

AC:

42517

AN:

152216

Hom.:

6275

Cov.:

AF XY:

0.278

AC XY:

20694

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.364

AC:

15097

AN:

41520

American (AMR)

AF:

0.212

AC:

3246

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

687

AN:

3470

East Asian (EAS)

AF:

0.287

AC:

1483

AN:

5176

South Asian (SAS)

AF:

0.285

AC:

1378

AN:

4832

European-Finnish (FIN)

AF:

0.265

AC:

2814

AN:

10600

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.249

AC:

16899

AN:

67994

Other (OTH)

AF:

0.266

AC:

563

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1581

3162

4742

6323

7904

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<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:

0.257

Hom.:

22510

Bravo

AF:

0.276

Asia WGS

AF:

0.306

AC:

1062

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

(source)

DANN

Benign

0.38

PhyloP100

-0.37

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.

Publications

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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