Variant rs7590705 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000454503.6(ENSG00000231731):n.76A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,528 control chromosomes in the GnomAD database, including 24,981 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 0.56 ( 24960 hom., cov: 31)

Exomes 𝑓: 0.53 ( 21 hom. )

Consequence

ENST00000454503.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Variant links:

Genes affected

(HGNC:):

links:

IWS1 (HGNC:25467): (interacts with SUPT6H, CTD assembly factor 1) Involved in regulation of histone modification; regulation of mRNA export from nucleus; and regulation of mRNA processing. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

IWS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.02).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.732 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
	ENST00000454503.6 linkuse as main transcript	n.76A>G	non_coding_transcript_exon_variant	1/3	2
	ENST00000626634.2 linkuse as main transcript	n.68A>G	non_coding_transcript_exon_variant	1/5	5
IWS1	ENST00000412979.1 linkuse as main transcript	c.*248+2334T>C	intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.558

AC:

84364

AN:

151282

Hom.:

24911

Cov.:

show subpopulations

Gnomad AFR

AF:

0.739

Gnomad AMI

AF:

0.366

Gnomad AMR

AF:

0.440

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.586

Gnomad FIN

AF:

0.516

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.499

Gnomad OTH

AF:

0.563

GnomAD4 exome

AF:

0.531

AC:

AN:

128

Hom.:

Cov.:

AF XY:

0.560

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

1.00

Gnomad4 ASJ exome

AF:

1.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.588

Gnomad4 NFE exome

AF:

0.471

Gnomad4 OTH exome

AF:

0.667

GnomAD4 genome

AF:

0.558

AC:

84473

AN:

151400

Hom.:

24960

Cov.:

AF XY:

0.556

AC XY:

41171

AN XY:

74022

show subpopulations

Gnomad4 AFR

AF:

0.739

Gnomad4 AMR

AF:

0.440

Gnomad4 ASJ

AF:

0.431

Gnomad4 EAS

AF:

0.425

Gnomad4 SAS

AF:

0.587

Gnomad4 FIN

AF:

0.516

Gnomad4 NFE

AF:

0.499

Gnomad4 OTH

AF:

0.569

Alfa

AF:

0.506

Hom.:

28460

Bravo

AF:

0.556

Asia WGS

AF:

0.547

AC:

1905

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.44

DANN

Benign

0.36

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