Variant 4-183517570-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The 4-183517570-G-T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 151,678 control chromosomes in the GnomAD database, including 5,170 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 0.26 ( 5167 hom., cov: 31)

Exomes 𝑓: 0.19 ( 3 hom. )

Consequence

ENST00000608204.1 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.26

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.04).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 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
	ENST00000608204.1 linkuse as main transcript			downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38625

AN:

151314

Hom.:

5173

Cov.:

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.216

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.444

Gnomad SAS

AF:

0.238

Gnomad FIN

AF:

0.303

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.219

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.187

AC:

AN:

246

Hom.:

Cov.:

AF XY:

0.176

AC XY:

AN XY:

188

show subpopulations

Gnomad4 AFR exome

AF:

0.250

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.250

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.161

Gnomad4 OTH exome

AF:

0.182

GnomAD4 genome

AF:

0.255

AC:

38628

AN:

151432

Hom.:

5167

Cov.:

AF XY:

0.260

AC XY:

19252

AN XY:

73940

show subpopulations

Gnomad4 AFR

AF:

0.283

Gnomad4 AMR

AF:

0.216

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.443

Gnomad4 SAS

AF:

0.237

Gnomad4 FIN

AF:

0.303

Gnomad4 NFE

AF:

0.219

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.223

Hom.:

1500

Bravo

AF:

0.252

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.24

DANN

Benign

0.49

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