Variant chr6-14988536-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 ENST00000437648.1(ENSG00000234261):n.486+8880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,916 control chromosomes in the GnomAD database, including 13,246 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 0.40 ( 13246 hom., cov: 31)

Consequence

ENSG00000234261
ENST00000437648.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.78

Variant links:

Genes affected

ENSG00000234261 (HGNC:):

ENSG00000234261 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374945	XR_007059473.1 link	n.220+8880A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000234261	ENST00000437648.1 link	n.486+8880A>G	intron_variant	5
ENSG00000234261	ENST00000629853.2 link	n.204+8880A>G	intron_variant	5
ENSG00000234261	ENST00000653525.1 link	n.397+8880A>G	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.395

AC:

59980

AN:

151796

Hom.:

13204

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.438

Gnomad AMR

AF:

0.351

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.330

Gnomad SAS

AF:

0.596

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.303

Gnomad NFE

AF:

0.289

Gnomad OTH

AF:

0.375

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

GnomAD4 genome

AF:

0.395

AC:

60082

AN:

151916

Hom.:

13246

Cov.:

AF XY:

0.398

AC XY:

29556

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.597

Gnomad4 AMR

AF:

0.351

Gnomad4 ASJ

AF:

0.405

Gnomad4 EAS

AF:

0.330

Gnomad4 SAS

AF:

0.597

Gnomad4 FIN

AF:

0.297

Gnomad4 NFE

AF:

0.289

Gnomad4 OTH

AF:

0.377

Alfa

AF:

0.311

Hom.:

16125

Bravo

AF:

0.400

Asia WGS

AF:

0.491

AC:

1706

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.33

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