Genetic Variant ENSG00000228876:n.965+49119C>T (chr2-16278385-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000420404.2(ENSG00000228876):n.965+49119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 152,002 control chromosomes in the GnomAD database, including 23,162 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 0.54 ( 23151 hom., cov: 31)

Exomes 𝑓: 0.53 ( 11 hom. )

Consequence

ENSG00000228876
ENST00000420404.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.66

Publications

5 publications found

Variant links:

Genes affected

ENSG00000228876 (HGNC:):

ENSG00000228876 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000228876	ENST00000420404.2 link	n.965+49119C>T	intron_variant	Intron 3 of 3	3
ENSG00000228876	ENST00000642208.1 link	n.294-20456C>T	intron_variant	Intron 2 of 2
ENSG00000228876	ENST00000644340.1 link	n.286-142C>T	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.540

AC:

81950

AN:

151804

Hom.:

23126

Cov.:

show subpopulations

Gnomad AFR

AF:

0.655

Gnomad AMI

AF:

0.384

Gnomad AMR

AF:

0.542

Gnomad ASJ

AF:

0.491

Gnomad EAS

AF:

0.826

Gnomad SAS

AF:

0.740

Gnomad FIN

AF:

0.488

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.448

Gnomad OTH

AF:

0.498

GnomAD4 exome

AF:

0.525

AC:

AN:

Hom.:

AF XY:

0.519

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.469

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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

GnomAD4 genome

AF:

0.540

AC:

82023

AN:

151922

Hom.:

23151

Cov.:

AF XY:

0.547

AC XY:

40591

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.654

AC:

27083

AN:

41412

American (AMR)

AF:

0.542

AC:

8278

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.491

AC:

1705

AN:

3470

East Asian (EAS)

AF:

0.826

AC:

4254

AN:

5148

South Asian (SAS)

AF:

0.741

AC:

3564

AN:

4812

European-Finnish (FIN)

AF:

0.488

AC:

5144

AN:

10550

Middle Eastern (MID)

AF:

0.483

AC:

142

AN:

294

European-Non Finnish (NFE)

AF:

0.448

AC:

30442

AN:

67952

Other (OTH)

AF:

0.503

AC:

1061

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1838

3676

5514

7352

9190

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

702

1404

2106

2808

3510

<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:

0.478

Hom.:

66741

Bravo

AF:

0.543

Asia WGS

AF:

0.780

AC:

2711

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.36

(source)

DANN

Benign

0.65

PhyloP100

-1.7

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over