Variant chr14-39627781-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000652126.1(ENSG00000258526):n.153-27723A>G 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 0.416 in 152,020 control chromosomes in the GnomAD database, including 14,528 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 0.42 ( 14528 hom., cov: 32)

Consequence

ENST00000652126.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.746

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370461	XR_001750723.2 linkuse as main transcript	n.167-27064A>G		intron_variant, non_coding_transcript_variant

Ensembl

Transcript	HGVSc	Effect
ENST00000652126.1 linkuse as main transcript	n.153-27723A>G	intron_variant, non_coding_transcript_variant
ENST00000650911.1 linkuse as main transcript	n.113-27723A>G	intron_variant, non_coding_transcript_variant
ENST00000651829.1 linkuse as main transcript	n.641-14932A>G	intron_variant, non_coding_transcript_variant
ENST00000662828.1 linkuse as main transcript	n.115-27723A>G	intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.416

AC:

63232

AN:

151902

Hom.:

14512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.613

Gnomad AMI

AF:

0.285

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.214

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.495

Gnomad FIN

AF:

0.386

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.359

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

GnomAD4 genome

AF:

0.416

AC:

63299

AN:

152020

Hom.:

14528

Cov.:

AF XY:

0.418

AC XY:

31090

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.613

Gnomad4 AMR

AF:

0.350

Gnomad4 ASJ

AF:

0.214

Gnomad4 EAS

AF:

0.453

Gnomad4 SAS

AF:

0.493

Gnomad4 FIN

AF:

0.386

Gnomad4 NFE

AF:

0.322

Gnomad4 OTH

AF:

0.365

Alfa

AF:

0.331

Hom.:

17733

Bravo

AF:

0.416

Asia WGS

AF:

0.510

AC:

1776

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

6.4

DANN

Benign

0.73

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