Genetic Variant ENST00000769348.1:n.164+2374T>C (chr16-89600929-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000769348.1(ENSG00000300127):n.164+2374T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,146 control chromosomes in the GnomAD database, including 9,467 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 0.33 ( 9467 hom., cov: 33)

Consequence

ENSG00000300127
ENST00000769348.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.873

Publications

38 publications found

Variant links:

Genes affected

ENSG00000300127 (HGNC:):

ENSG00000300127 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=-1.0).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000300127	ENST00000769348.1 link	n.164+2374T>C	intron_variant	Intron 1 of 3
ENSG00000300127	ENST00000769349.1 link	n.189+2322T>C	intron_variant	Intron 1 of 3
ENSG00000300127	ENST00000769350.1 link	n.185+2322T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.334

AC:

50828

AN:

152030

Hom.:

9433

Cov.:

show subpopulations

Gnomad AFR

AF:

0.496

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.359

Gnomad ASJ

AF:

0.276

Gnomad EAS

AF:

0.387

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.136

Gnomad NFE

AF:

0.245

Gnomad OTH

AF:

0.283

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

GnomAD4 genome

AF:

0.335

AC:

50930

AN:

152146

Hom.:

9467

Cov.:

AF XY:

0.336

AC XY:

24962

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.496

AC:

20585

AN:

41484

American (AMR)

AF:

0.360

AC:

5496

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.276

AC:

957

AN:

3466

East Asian (EAS)

AF:

0.386

AC:

1998

AN:

5170

South Asian (SAS)

AF:

0.288

AC:

1387

AN:

4820

European-Finnish (FIN)

AF:

0.293

AC:

3107

AN:

10614

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.245

AC:

16632

AN:

67992

Other (OTH)

AF:

0.289

AC:

610

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1653

3306

4960

6613

8266

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

474

948

1422

1896

2370

<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:

0.276

Hom.:

26766

Bravo

AF:

0.351

Asia WGS

AF:

0.409

AC:

1420

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.58

(source)

DANN

Benign

0.51

PhyloP100

-0.87

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over