Genetic Variant ENST00000562178.1:n.193-3915A>T (chr16-53039876-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000562178.1(CHD9NB):n.193-3915A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,826 control chromosomes in the GnomAD database, including 21,405 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 0.53 ( 21405 hom., cov: 31)

Consequence

CHD9NB
ENST00000562178.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.559

Publications

3 publications found

Variant links:

Genes affected

CHD9NB (HGNC:53436): (CHD9 neighbor)

CHD9NB links:

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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=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHD9NB	NR_136518.1 link	n.193-3915A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CHD9NB	ENST00000562178.1 link	n.193-3915A>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.528

AC:

80027

AN:

151708

Hom.:

21388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.586

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.511

Gnomad ASJ

AF:

0.542

Gnomad EAS

AF:

0.653

Gnomad SAS

AF:

0.505

Gnomad FIN

AF:

0.442

Gnomad MID

AF:

0.614

Gnomad NFE

AF:

0.500

Gnomad OTH

AF:

0.537

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

GnomAD4 genome

AF:

0.527

AC:

80085

AN:

151826

Hom.:

21405

Cov.:

AF XY:

0.527

AC XY:

39108

AN XY:

74162

show subpopulations

African (AFR)

AF:

0.586

AC:

24283

AN:

41414

American (AMR)

AF:

0.511

AC:

7787

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.542

AC:

1879

AN:

3466

East Asian (EAS)

AF:

0.652

AC:

3369

AN:

5164

South Asian (SAS)

AF:

0.504

AC:

2425

AN:

4812

European-Finnish (FIN)

AF:

0.442

AC:

4635

AN:

10492

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.500

AC:

33975

AN:

67914

Other (OTH)

AF:

0.543

AC:

1144

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1895

3790

5684

7579

9474

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.337

Hom.:

748

Bravo

AF:

0.538

Asia WGS

AF:

0.590

AC:

2047

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.1

(source)

DANN

Benign

0.85

PhyloP100

0.56

Splicing

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

Publications

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ENST00000562178.1:n.193-3915A>T

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over