Genetic Variant ENST00000444936.3:n.313+98C>T (chr9-134520718-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 ENST00000444936.3(ENSG00000228877):n.313+98C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,008 control chromosomes in the GnomAD database, including 10,736 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 0.37 ( 10735 hom., cov: 32)

Exomes 𝑓: 0.67 ( 1 hom. )

Consequence

ENSG00000228877
ENST00000444936.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

3 publications found

Variant links:

Genes affected

ENSG00000228877 (HGNC:):

ENSG00000228877 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 = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100506532	NR_188441.1 link	n.183+15172C>T		intron_variant	Intron 2 of 2
LOC100506532	NR_188442.1 link	n.612+98C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000228877	ENST00000444936.3 link	n.313+98C>T	intron_variant	Intron 3 of 3	2
ENSG00000228877	ENST00000745249.1 link	n.1011+15172C>T	intron_variant	Intron 7 of 7
ENSG00000228877	ENST00000745250.1 link	n.270+15172C>T	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.370

AC:

56216

AN:

151884

Hom.:

10739

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.490

Gnomad AMR

AF:

0.436

Gnomad ASJ

AF:

0.458

Gnomad EAS

AF:

0.437

Gnomad SAS

AF:

0.323

Gnomad FIN

AF:

0.326

Gnomad MID

AF:

0.471

Gnomad NFE

AF:

0.398

Gnomad OTH

AF:

0.393

GnomAD4 exome

AF:

0.667

AC:

AN:

Hom.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.600

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.370

AC:

56240

AN:

152002

Hom.:

10735

Cov.:

AF XY:

0.368

AC XY:

27341

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.296

AC:

12274

AN:

41438

American (AMR)

AF:

0.436

AC:

6662

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.458

AC:

1587

AN:

3466

East Asian (EAS)

AF:

0.436

AC:

2252

AN:

5160

South Asian (SAS)

AF:

0.323

AC:

1552

AN:

4806

European-Finnish (FIN)

AF:

0.326

AC:

3436

AN:

10556

Middle Eastern (MID)

AF:

0.469

AC:

137

AN:

292

European-Non Finnish (NFE)

AF:

0.398

AC:

27069

AN:

67970

Other (OTH)

AF:

0.391

AC:

825

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1825

3650

5474

7299

9124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

552

1104

1656

2208

2760

<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:

0.380

Hom.:

1441

Bravo

AF:

0.380

Asia WGS

AF:

0.387

AC:

1345

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

0.67

(source)

DANN

Benign

0.23

PhyloP100

-1.4

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