Variant rs2307924 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000648938.1(ENSG00000285718):n.250+11241_250+11242insTATTTAAT 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 0.53 ( 21485 hom., cov: 0)

Consequence

ENST00000648938.1 intron, non_coding_transcript

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.618

Variant links:

Genes affected

(HGNC:):

links:

Genome browser will be placed here

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 = 0.659 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
	ENST00000648938.1 linkuse as main transcript	n.250+11241_250+11242insTATTTAAT		intron_variant, non_coding_transcript_variant
	ENST00000670710.1 linkuse as main transcript	n.216+11241_216+11242insTATTTAAT		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.525

AC:

79327

AN:

151054

Hom.:

21450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.354

Gnomad AMR

AF:

0.443

Gnomad ASJ

AF:

0.481

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.491

Gnomad FIN

AF:

0.561

Gnomad MID

AF:

0.477

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.505

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

GnomAD4 genome

AF:

0.525

AC:

79411

AN:

151174

Hom.:

21485

Cov.:

AF XY:

0.525

AC XY:

38739

AN XY:

73806

show subpopulations

Gnomad4 AFR

AF:

0.665

Gnomad4 AMR

AF:

0.442

Gnomad4 ASJ

AF:

0.481

Gnomad4 EAS

AF:

0.316

Gnomad4 SAS

AF:

0.491

Gnomad4 FIN

AF:

0.561

Gnomad4 NFE

AF:

0.477

Gnomad4 OTH

AF:

0.507

Alfa

AF:

0.340

Hom.:

650

Asia WGS

AF:

0.414

AC:

1439

AN:

3474

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