Genetic Variant ENST00000747913.1:n.296+126T>A (chr4-165506259-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000747913.1(ENSG00000297440):n.296+126T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 152,154 control chromosomes in the GnomAD database, including 13,063 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 0.31 ( 13063 hom., cov: 33)

Consequence

ENSG00000297440
ENST00000747913.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.808

Publications

9 publications found

Variant links:

Genes affected

ENSG00000297440 (HGNC:):

ENSG00000297440 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377520	XR_939419.2 link	n.233+126T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000297440	ENST00000747913.1 link	n.296+126T>A	intron_variant	Intron 3 of 3
ENSG00000297440	ENST00000747914.1 link	n.184+126T>A	intron_variant	Intron 2 of 2
ENSG00000297440	ENST00000747915.1 link	n.292+126T>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.311

AC:

47256

AN:

152036

Hom.:

13016

Cov.:

show subpopulations

Gnomad AFR

AF:

0.747

Gnomad AMI

AF:

0.0450

Gnomad AMR

AF:

0.187

Gnomad ASJ

AF:

0.117

Gnomad EAS

AF:

0.320

Gnomad SAS

AF:

0.150

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.241

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

GnomAD4 genome

AF:

0.311

AC:

47356

AN:

152154

Hom.:

13063

Cov.:

AF XY:

0.306

AC XY:

22782

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.748

AC:

31010

AN:

41468

American (AMR)

AF:

0.187

AC:

2860

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.117

AC:

405

AN:

3462

East Asian (EAS)

AF:

0.320

AC:

1657

AN:

5180

South Asian (SAS)

AF:

0.149

AC:

717

AN:

4820

European-Finnish (FIN)

AF:

0.164

AC:

1744

AN:

10604

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8370

AN:

68014

Other (OTH)

AF:

0.241

AC:

510

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1116

2232

3347

4463

5579

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<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:

0.235

Hom.:

1027

Bravo

AF:

0.332

Asia WGS

AF:

0.285

AC:

990

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

2.9

(source)

DANN

Benign

0.47

PhyloP100

0.81

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