Genetic Variant ENSG00000309145:n.434+10919C>T (chr4-130044017-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 ENST00000839037.1(ENSG00000309145):n.434+10919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,126 control chromosomes in the GnomAD database, including 4,540 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 0.15 ( 4540 hom., cov: 32)

Consequence

ENSG00000309145
ENST00000839037.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.365

Publications

1 publications found

Variant links:

Genes affected

ENSG00000309145 (HGNC:):

ENSG00000309145 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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
ENSG00000309145	ENST00000839037.1 link	n.434+10919C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes

AF:

0.148

AC:

22558

AN:

152010

Hom.:

4525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.459

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0906

Gnomad ASJ

AF:

0.00663

Gnomad EAS

AF:

0.0711

Gnomad SAS

AF:

0.0460

Gnomad FIN

AF:

0.0581

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.0108

Gnomad OTH

AF:

0.115

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

GnomAD4 genome

AF:

0.149

AC:

22620

AN:

152126

Hom.:

4540

Cov.:

AF XY:

0.146

AC XY:

10884

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.459

AC:

18999

AN:

41434

American (AMR)

AF:

0.0903

AC:

1381

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00663

AC:

AN:

3470

East Asian (EAS)

AF:

0.0714

AC:

369

AN:

5166

South Asian (SAS)

AF:

0.0468

AC:

226

AN:

4824

European-Finnish (FIN)

AF:

0.0581

AC:

616

AN:

10602

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0108

AC:

736

AN:

68022

Other (OTH)

AF:

0.121

AC:

255

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

704

1408

2113

2817

3521

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.0260

Hom.:

117

Bravo

AF:

0.164

Asia WGS

AF:

0.100

AC:

349

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.7

(source)

DANN

Benign

0.81

PhyloP100

-0.36

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