Genetic Variant ENST00000507514.1:n.39+388_39+389insCTTCCCGCGGCCG (chr5-76715788-A-ACGGCCGCGGGAAG) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000507514.1(ENSG00000225407):n.39+388_39+389insCTTCCCGCGGCCG variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 8801 hom., cov: 0)

Consequence

ENSG00000225407
ENST00000507514.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.351

Publications

12 publications found

Variant links:

Genes affected

ENSG00000225407 (HGNC:):

ENSG00000225407 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507514.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225407	ENST00000507514.1	TSL:3	n.39+388_39+389insCTTCCCGCGGCCG		intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47308

AN:

151716

Hom.:

8777

Cov.:

show subpopulations

Gnomad AFR

AF:

0.517

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.0311

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.243

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.288

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

GnomAD4 genome

AF:

0.312

AC:

47375

AN:

151826

Hom.:

8801

Cov.:

AF XY:

0.311

AC XY:

23083

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.517

AC:

21379

AN:

41358

American (AMR)

AF:

0.232

AC:

3539

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.314

AC:

1085

AN:

3460

East Asian (EAS)

AF:

0.0310

AC:

160

AN:

5158

South Asian (SAS)

AF:

0.392

AC:

1878

AN:

4792

European-Finnish (FIN)

AF:

0.243

AC:

2578

AN:

10592

Middle Eastern (MID)

AF:

0.353

AC:

103

AN:

292

European-Non Finnish (NFE)

AF:

0.232

AC:

15769

AN:

67874

Other (OTH)

AF:

0.284

AC:

600

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1482

2964

4445

5927

7409

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

448

896

1344

1792

2240

<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:

0.0912

Hom.:

104

Asia WGS

AF:

0.253

AC:

879

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.35

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over