Genetic Variant :null (chr16-56961324-C-A) – 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 0.515 in 481,042 control chromosomes in the GnomAD database, including 64,531 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 0.52 ( 20884 hom., cov: 33)

Exomes 𝑓: 0.51 ( 43647 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0920

Publications

278 publications found

Variant links:

COSMIC-nc: COSV52363979

Genome browser will be placed here

ACMG classification

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 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:

0.522

AC:

79285

AN:

151974

Hom.:

20854

Cov.:

show subpopulations

Gnomad AFR

AF:

0.575

Gnomad AMI

AF:

0.653

Gnomad AMR

AF:

0.506

Gnomad ASJ

AF:

0.504

Gnomad EAS

AF:

0.499

Gnomad SAS

AF:

0.601

Gnomad FIN

AF:

0.509

Gnomad MID

AF:

0.509

Gnomad NFE

AF:

0.490

Gnomad OTH

AF:

0.502

GnomAD2 exomes

AF:

0.508

AC:

88585

AN:

174424

AF XY:

0.511

show subpopulations

Gnomad AFR exome

AF:

0.558

Gnomad AMR exome

AF:

0.528

Gnomad ASJ exome

AF:

0.513

Gnomad EAS exome

AF:

0.491

Gnomad FIN exome

AF:

0.467

Gnomad NFE exome

AF:

0.473

Gnomad OTH exome

AF:

0.500

GnomAD4 exome

AF:

0.512

AC:

168449

AN:

328950

Hom.:

43647

Cov.:

AF XY:

0.518

AC XY:

97232

AN XY:

187742

show subpopulations

African (AFR)

AF:

0.567

AC:

5509

AN:

9720

American (AMR)

AF:

0.528

AC:

16390

AN:

31054

Ashkenazi Jewish (ASJ)

AF:

0.511

AC:

5702

AN:

11156

East Asian (EAS)

AF:

0.500

AC:

5861

AN:

11726

South Asian (SAS)

AF:

0.598

AC:

36785

AN:

61554

European-Finnish (FIN)

AF:

0.490

AC:

7146

AN:

14598

Middle Eastern (MID)

AF:

0.496

AC:

1378

AN:

2780

European-Non Finnish (NFE)

AF:

0.479

AC:

82028

AN:

171172

Other (OTH)

AF:

0.504

AC:

7650

AN:

15190

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.461

Heterozygous variant carriers

3858

7717

11575

15434

19292

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

642

1284

1926

2568

3210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.522

AC:

79359

AN:

152092

Hom.:

20884

Cov.:

AF XY:

0.525

AC XY:

39066

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.576

AC:

23875

AN:

41480

American (AMR)

AF:

0.506

AC:

7738

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.504

AC:

1748

AN:

3468

East Asian (EAS)

AF:

0.498

AC:

2582

AN:

5180

South Asian (SAS)

AF:

0.601

AC:

2897

AN:

4824

European-Finnish (FIN)

AF:

0.509

AC:

5385

AN:

10572

Middle Eastern (MID)

AF:

0.490

AC:

144

AN:

294

European-Non Finnish (NFE)

AF:

0.490

AC:

33337

AN:

67970

Other (OTH)

AF:

0.502

AC:

1059

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

2040

4080

6121

8161

10201

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.499

Hom.:

85619

Bravo

AF:

0.522

Asia WGS

AF:

0.546

AC:

1902

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.41

(source)

DANN

Benign

0.66

PhyloP100

-0.092

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over