Variant 5-156963286-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 variant allele was found at a frequency of 0.632 in 1,400,670 control chromosomes in the GnomAD database, including 283,865 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 0.57 ( 26155 hom., cov: 31)

Exomes 𝑓: 0.64 ( 257710 hom. )

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.15

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=-0.79).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.156963286T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.572

AC:

86800

AN:

151852

Hom.:

26139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.367

Gnomad AMI

AF:

0.819

Gnomad AMR

AF:

0.685

Gnomad ASJ

AF:

0.612

Gnomad EAS

AF:

0.744

Gnomad SAS

AF:

0.676

Gnomad FIN

AF:

0.684

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.627

Gnomad OTH

AF:

0.581

GnomAD4 exome

AF:

0.640

AC:

798631

AN:

1248700

Hom.:

257710

Cov.:

AF XY:

0.640

AC XY:

404648

AN XY:

632002

show subpopulations

Gnomad4 AFR exome

AF:

0.355

Gnomad4 AMR exome

AF:

0.790

Gnomad4 ASJ exome

AF:

0.616

Gnomad4 EAS exome

AF:

0.784

Gnomad4 SAS exome

AF:

0.662

Gnomad4 FIN exome

AF:

0.663

Gnomad4 NFE exome

AF:

0.635

Gnomad4 OTH exome

AF:

0.616

GnomAD4 genome

AF:

0.571

AC:

86844

AN:

151970

Hom.:

26155

Cov.:

AF XY:

0.579

AC XY:

43022

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.366

Gnomad4 AMR

AF:

0.685

Gnomad4 ASJ

AF:

0.612

Gnomad4 EAS

AF:

0.745

Gnomad4 SAS

AF:

0.677

Gnomad4 FIN

AF:

0.684

Gnomad4 NFE

AF:

0.627

Gnomad4 OTH

AF:

0.585

Alfa

AF:

0.626

Hom.:

57334

Bravo

AF:

0.564

Asia WGS

AF:

0.690

AC:

2402

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

DANN

Benign

0.57

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