Variant 5-76715788-ACGGCCGCGGGAAG-ACGGCCGCGGGAAGCGGCCGCGGGAAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The ENST00000507514.1(ENSG00000225407):n.39+388_39+389insCTTCCCGCGGCCG variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 8801 hom., cov: 0)

Consequence

ENST00000507514.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.351

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000507514.1 linkuse as main transcript	n.39+388_39+389insCTTCCCGCGGCCG		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR

AF:

0.517

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.314

Gnomad4 EAS

AF:

0.0310

Gnomad4 SAS

AF:

0.392

Gnomad4 FIN

AF:

0.243

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.284

Alfa

AF:

0.0912

Hom.:

104

Asia WGS

AF:

0.253

AC:

879

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over