Variant chr6-31272264-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000692808.1(ENSG00000288813):n.25C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 398,996 control chromosomes in the GnomAD database, including 57,148 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 0.56 ( 21454 hom., cov: 20)

Exomes 𝑓: 0.49 ( 35694 hom. )

Consequence

ENSG00000288813
ENST00000692808.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.219

Variant links:

Genes affected

ENSG00000288813 (HGNC:):

ENSG00000288813 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.31272264C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288813	ENST00000692808.1 linkuse as main transcript	n.25C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.556

AC:

75687

AN:

136236

Hom.:

21451

Cov.:

show subpopulations

Gnomad AFR

AF:

0.501

Gnomad AMI

AF:

0.507

Gnomad AMR

AF:

0.563

Gnomad ASJ

AF:

0.655

Gnomad EAS

AF:

0.744

Gnomad SAS

AF:

0.613

Gnomad FIN

AF:

0.506

Gnomad MID

AF:

0.567

Gnomad NFE

AF:

0.570

Gnomad OTH

AF:

0.554

GnomAD4 exome

AF:

0.489

AC:

128496

AN:

262654

Hom.:

35694

AF XY:

0.492

AC XY:

67608

AN XY:

137502

show subpopulations

Gnomad4 AFR exome

AF:

0.405

Gnomad4 AMR exome

AF:

0.481

Gnomad4 ASJ exome

AF:

0.569

Gnomad4 EAS exome

AF:

0.726

Gnomad4 SAS exome

AF:

0.580

Gnomad4 FIN exome

AF:

0.389

Gnomad4 NFE exome

AF:

0.458

Gnomad4 OTH exome

AF:

0.484

GnomAD4 genome

AF:

0.555

AC:

75717

AN:

136342

Hom.:

21454

Cov.:

AF XY:

0.554

AC XY:

36432

AN XY:

65782

show subpopulations

Gnomad4 AFR

AF:

0.500

Gnomad4 AMR

AF:

0.563

Gnomad4 ASJ

AF:

0.655

Gnomad4 EAS

AF:

0.745

Gnomad4 SAS

AF:

0.611

Gnomad4 FIN

AF:

0.506

Gnomad4 NFE

AF:

0.570

Gnomad4 OTH

AF:

0.553

Alfa

AF:

0.551

Hom.:

1734

Asia WGS

AF:

0.638

AC:

2220

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

DANN

Benign

0.90

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