Genetic Variant ENSG00000289844:n.58+11347T>C (chr14-75347325-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 ENST00000749181.1(ENSG00000289844):n.58+11347T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,274 control chromosomes in the GnomAD database, including 2,014 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 0.14 ( 2014 hom., cov: 32)

Consequence

ENSG00000289844
ENST00000749181.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.564

Publications

5 publications found

Variant links:

Genes affected

ENSG00000289844 (HGNC:):

ENSG00000289844 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=-0.87).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289844	ENST00000749181.1 link	n.58+11347T>C		intron_variant	Intron 1 of 1
ENSG00000289844	ENST00000749182.1 link	n.55-4757T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21845

AN:

152156

Hom.:

2004

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0418

Gnomad AMI

AF:

0.209

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.194

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.249

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.161

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.144

AC:

21862

AN:

152274

Hom.:

2014

Cov.:

AF XY:

0.148

AC XY:

10994

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.0416

AC:

1729

AN:

41566

American (AMR)

AF:

0.245

AC:

3753

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.194

AC:

673

AN:

3470

East Asian (EAS)

AF:

0.182

AC:

944

AN:

5188

South Asian (SAS)

AF:

0.248

AC:

1196

AN:

4816

European-Finnish (FIN)

AF:

0.195

AC:

2071

AN:

10598

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.161

AC:

10973

AN:

68018

Other (OTH)

AF:

0.130

AC:

275

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

908

1817

2725

3634

4542

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.151

Hom.:

263

Bravo

AF:

0.145

Asia WGS

AF:

0.190

AC:

661

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

4.9

(source)

DANN

Benign

0.91

PhyloP100

0.56

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