Variant 16-49319593-A-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000643467.1(ENSG00000279249):n.659-10874A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 151,268 control chromosomes in the GnomAD database, including 38,225 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 0.69 ( 38225 hom., cov: 30)

Consequence

ENSG00000279249
ENST00000643467.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.248

Variant links:

Genes affected

ENSG00000279249 (HGNC:56730):

ENSG00000279249 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
ENSG00000279249	ENST00000564048.2 link	n.136-10874A>T	intron_variant	6
ENSG00000279249	ENST00000623424.2 link	n.197-10874A>T	intron_variant	6
ENSG00000279249	ENST00000643467.1 link	n.659-10874A>T	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.694

AC:

104881

AN:

151152

Hom.:

38168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.868

Gnomad AMI

AF:

0.674

Gnomad AMR

AF:

0.760

Gnomad ASJ

AF:

0.671

Gnomad EAS

AF:

0.984

Gnomad SAS

AF:

0.788

Gnomad FIN

AF:

0.498

Gnomad MID

AF:

0.696

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.717

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

GnomAD4 genome

AF:

0.694

AC:

104994

AN:

151268

Hom.:

38225

Cov.:

AF XY:

0.697

AC XY:

51500

AN XY:

73900

show subpopulations

Gnomad4 AFR

AF:

0.869

Gnomad4 AMR

AF:

0.760

Gnomad4 ASJ

AF:

0.671

Gnomad4 EAS

AF:

0.983

Gnomad4 SAS

AF:

0.786

Gnomad4 FIN

AF:

0.498

Gnomad4 NFE

AF:

0.574

Gnomad4 OTH

AF:

0.721

Alfa

AF:

0.601

Hom.:

3446

Bravo

AF:

0.727

Asia WGS

AF:

0.873

AC:

3028

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.1

DANN

Benign

0.82

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