Variant rs4602918 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000520024.1(ENSG00000253853):n.176+38038T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,994 control chromosomes in the GnomAD database, including 20,560 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 0.45 ( 20560 hom., cov: 33)

Consequence

ENSG00000253853
ENST00000520024.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.152

Variant links:

Genes affected

ENSG00000253853 (HGNC:):

ENSG00000253853 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=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
LOC105377785	NR_168441.1 link	n.538+38038T>C	intron_variant
LOC105377785	NR_168442.1 link	n.538+38038T>C	intron_variant
LOC105377785	NR_168443.1 link	n.538+38038T>C	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000253853	ENST00000520024.1 link	n.176+38038T>C	intron_variant	3
ENSG00000253853	ENST00000654515.1 link	n.531+38038T>C	intron_variant
ENSG00000253853	ENST00000670600.1 link	n.538+38038T>C	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.451

AC:

68551

AN:

151876

Hom.:

20504

Cov.:

show subpopulations

Gnomad AFR

AF:

0.843

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.509

Gnomad ASJ

AF:

0.332

Gnomad EAS

AF:

0.519

Gnomad SAS

AF:

0.295

Gnomad FIN

AF:

0.255

Gnomad MID

AF:

0.430

Gnomad NFE

AF:

0.246

Gnomad OTH

AF:

0.415

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

GnomAD4 genome

AF:

0.452

AC:

68665

AN:

151994

Hom.:

20560

Cov.:

AF XY:

0.454

AC XY:

33706

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.844

Gnomad4 AMR

AF:

0.510

Gnomad4 ASJ

AF:

0.332

Gnomad4 EAS

AF:

0.519

Gnomad4 SAS

AF:

0.293

Gnomad4 FIN

AF:

0.255

Gnomad4 NFE

AF:

0.246

Gnomad4 OTH

AF:

0.417

Alfa

AF:

0.358

Hom.:

1691

Bravo

AF:

0.492

Asia WGS

AF:

0.437

AC:

1517

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.63

DANN

Benign

0.51

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