Variant rs12654778 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1

The variant allele was found at a frequency of 0.345 in 155,164 control chromosomes in the GnomAD database, including 9,773 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 9503 hom., cov: 31)

Exomes 𝑓: 0.36 ( 270 hom. )

Consequence

Unknown

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.60

Variant links:

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ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 5-148826178-G-A is Benign according to our data. Variant chr5-148826178-G-A is described in ClinVar as [Benign]. Clinvar id is 1180015.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.344

AC:

52246

AN:

151672

Hom.:

9487

Cov.:

show subpopulations

Gnomad AFR

AF:

0.237

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.387

Gnomad ASJ

AF:

0.415

Gnomad EAS

AF:

0.385

Gnomad SAS

AF:

0.388

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.357

GnomAD4 exome

AF:

0.363

AC:

1225

AN:

3374

Hom.:

270

Cov.:

AF XY:

0.357

AC XY:

646

AN XY:

1810

show subpopulations

Gnomad4 AFR exome

AF:

0.0556

Gnomad4 AMR exome

AF:

0.324

Gnomad4 ASJ exome

AF:

0.353

Gnomad4 EAS exome

AF:

0.188

Gnomad4 SAS exome

AF:

0.350

Gnomad4 FIN exome

AF:

0.422

Gnomad4 NFE exome

AF:

0.363

Gnomad4 OTH exome

AF:

0.371

GnomAD4 genome

AF:

0.344

AC:

52287

AN:

151790

Hom.:

9503

Cov.:

AF XY:

0.351

AC XY:

26058

AN XY:

74198

show subpopulations

Gnomad4 AFR

AF:

0.237

Gnomad4 AMR

AF:

0.388

Gnomad4 ASJ

AF:

0.415

Gnomad4 EAS

AF:

0.384

Gnomad4 SAS

AF:

0.390

Gnomad4 FIN

AF:

0.473

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.364

Alfa

AF:

0.365

Hom.:

20508

Bravo

AF:

0.332

Asia WGS

AF:

0.399

AC:

1383

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 09, 2019

This variant is associated with the following publications: (PMID: 29588580) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over