Variant 11-72181857-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.31 ( 0 hom., cov: 36)

Failed GnomAD Quality Control

Consequence

intergenic_region

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0550

Variant links:

Genes affected

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.72181857G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000204971	ENST00000378140.3 linkuse as main transcript	n.419+16656C>G		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

20138

AN:

65588

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.239

Gnomad AMI

AF:

0.426

Gnomad AMR

AF:

0.363

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.203

Gnomad SAS

AF:

0.261

Gnomad FIN

AF:

0.311

Gnomad MID

AF:

0.213

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.301

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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.307

AC:

20155

AN:

65670

Hom.:

Cov.:

AF XY:

0.307

AC XY:

10135

AN XY:

32980

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.363

Gnomad4 ASJ

AF:

0.340

Gnomad4 EAS

AF:

0.203

Gnomad4 SAS

AF:

0.263

Gnomad4 FIN

AF:

0.311

Gnomad4 NFE

AF:

0.353

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.345

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

8.4

DANN

Benign

0.63

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