Genetic Variant ENSG00000295400:n.387-1223T>C (chr5-149657413-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 ENST00000729811.1(ENSG00000295400):n.387-1223T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,254 control chromosomes in the GnomAD database, including 971 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 0.10 ( 971 hom., cov: 32)

Consequence

ENSG00000295400
ENST00000729811.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.285

Publications

11 publications found

Variant links:

Genes affected

ENSG00000295400 (HGNC:):

ENSG00000295400 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 (SAS) allele frequency at 95% confidence interval = 0.16 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
ENSG00000295400	ENST00000729811.1 link	n.387-1223T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.100

AC:

15228

AN:

152136

Hom.:

971

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0234

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.156

Gnomad EAS

AF:

0.0795

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.123

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.126

Gnomad OTH

AF:

0.120

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

GnomAD4 genome

AF:

0.100

AC:

15221

AN:

152254

Hom.:

971

Cov.:

AF XY:

0.102

AC XY:

7599

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.0233

AC:

970

AN:

41568

American (AMR)

AF:

0.146

AC:

2233

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

542

AN:

3470

East Asian (EAS)

AF:

0.0787

AC:

408

AN:

5184

South Asian (SAS)

AF:

0.170

AC:

817

AN:

4816

European-Finnish (FIN)

AF:

0.123

AC:

1306

AN:

10600

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.126

AC:

8588

AN:

68010

Other (OTH)

AF:

0.122

AC:

257

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

698

1396

2093

2791

3489

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<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:

0.102

Hom.:

770

Bravo

AF:

0.100

Asia WGS

AF:

0.111

AC:

388

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.1

(source)

DANN

Benign

0.54

PhyloP100

-0.28

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