Variant 4-134073497-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000651116.1(ENSG00000286253):n.351+10346T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 152,018 control chromosomes in the GnomAD database, including 39,407 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 0.71 ( 39407 hom., cov: 32)

Consequence

ENST00000651116.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.54

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=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
PABPC4L	XR_001741133.2 linkuse as main transcript	n.2163+29872A>G	intron_variant, non_coding_transcript_variant
PABPC4L	XR_001741134.2 linkuse as main transcript	n.1841+29872A>G	intron_variant, non_coding_transcript_variant
PABPC4L	XR_001741135.2 linkuse as main transcript	n.1841+29872A>G	intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect
ENST00000651116.1 linkuse as main transcript	n.351+10346T>C	intron_variant, non_coding_transcript_variant
ENST00000658435.1 linkuse as main transcript	n.560+29872A>G	intron_variant, non_coding_transcript_variant
ENST00000658033.1 linkuse as main transcript	n.692+29872A>G	intron_variant, non_coding_transcript_variant
ENST00000668641.1 linkuse as main transcript	n.696+29872A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108597

AN:

151902

Hom.:

39370

Cov.:

show subpopulations

Gnomad AFR

AF:

0.785

Gnomad AMI

AF:

0.760

Gnomad AMR

AF:

0.710

Gnomad ASJ

AF:

0.582

Gnomad EAS

AF:

0.948

Gnomad SAS

AF:

0.661

Gnomad FIN

AF:

0.780

Gnomad MID

AF:

0.557

Gnomad NFE

AF:

0.658

Gnomad OTH

AF:

0.652

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

GnomAD4 genome

AF:

0.715

AC:

108685

AN:

152018

Hom.:

39407

Cov.:

AF XY:

0.722

AC XY:

53637

AN XY:

74304

show subpopulations

Gnomad4 AFR

AF:

0.785

Gnomad4 AMR

AF:

0.710

Gnomad4 ASJ

AF:

0.582

Gnomad4 EAS

AF:

0.948

Gnomad4 SAS

AF:

0.660

Gnomad4 FIN

AF:

0.780

Gnomad4 NFE

AF:

0.658

Gnomad4 OTH

AF:

0.654

Alfa

AF:

0.607

Hom.:

1793

Bravo

AF:

0.712

Asia WGS

AF:

0.779

AC:

2705

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.49

DANN

Benign

0.42

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