Genetic Variant ENST00000745740.1:n.379-25376A>C (chr6-75555926-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000745740.1(ENSG00000297132):n.379-25376A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 152,076 control chromosomes in the GnomAD database, including 951 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 0.11 ( 951 hom., cov: 32)

Consequence

ENSG00000297132
ENST00000745740.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.22

Publications

39 publications found

Variant links:

Genes affected

ENSG00000297132 (HGNC:):

ENSG00000297132 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=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297132	ENST00000745740.1 link	n.379-25376A>C	intron_variant	Intron 2 of 3
ENSG00000297132	ENST00000745741.1 link	n.387-25376A>C	intron_variant	Intron 2 of 3
ENSG00000297132	ENST00000745742.1 link	n.373-25376A>C	intron_variant	Intron 3 of 4
ENSG00000297132	ENST00000745743.1 link	n.327-25376A>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.108

AC:

16461

AN:

151958

Hom.:

949

Cov.:

show subpopulations

Gnomad AFR

AF:

0.123

Gnomad AMI

AF:

0.103

Gnomad AMR

AF:

0.0931

Gnomad ASJ

AF:

0.0942

Gnomad EAS

AF:

0.0395

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.128

Gnomad MID

AF:

0.102

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.105

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

GnomAD4 genome

AF:

0.108

AC:

16477

AN:

152076

Hom.:

951

Cov.:

AF XY:

0.108

AC XY:

8038

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.123

AC:

5115

AN:

41510

American (AMR)

AF:

0.0931

AC:

1423

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0942

AC:

327

AN:

3470

East Asian (EAS)

AF:

0.0398

AC:

206

AN:

5178

South Asian (SAS)

AF:

0.103

AC:

495

AN:

4822

European-Finnish (FIN)

AF:

0.128

AC:

1350

AN:

10542

Middle Eastern (MID)

AF:

0.0959

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.106

AC:

7220

AN:

67962

Other (OTH)

AF:

0.104

AC:

220

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

743

1485

2228

2970

3713

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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.:

3293

Bravo

AF:

0.104

Asia WGS

AF:

0.0730

AC:

255

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

(source)

DANN

Benign

0.66

PhyloP100

1.2

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