Variant 5-148826364-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The variant allele was found at a frequency of 0.669 in 190,996 control chromosomes in the GnomAD database, including 44,602 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.68 ( 36683 hom., cov: 32)

Exomes 𝑓: 0.62 ( 7919 hom. )

Consequence

Unknown

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0210

Variant links:

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ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 5-148826364-G-C is Benign according to our data. Variant chr5-148826364-G-C is described in ClinVar as [Benign]. Clinvar id is 1235095.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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:

0.683

AC:

103737

AN:

151960

Hom.:

36653

Cov.:

show subpopulations

Gnomad AFR

AF:

0.821

Gnomad AMI

AF:

0.554

Gnomad AMR

AF:

0.758

Gnomad ASJ

AF:

0.630

Gnomad EAS

AF:

0.910

Gnomad SAS

AF:

0.794

Gnomad FIN

AF:

0.633

Gnomad MID

AF:

0.759

Gnomad NFE

AF:

0.568

Gnomad OTH

AF:

0.690

GnomAD4 exome

AF:

0.616

AC:

23991

AN:

38918

Hom.:

7919

Cov.:

AF XY:

0.630

AC XY:

12679

AN XY:

20110

show subpopulations

Gnomad4 AFR exome

AF:

0.833

Gnomad4 AMR exome

AF:

0.797

Gnomad4 ASJ exome

AF:

0.613

Gnomad4 EAS exome

AF:

0.901

Gnomad4 SAS exome

AF:

0.776

Gnomad4 FIN exome

AF:

0.592

Gnomad4 NFE exome

AF:

0.537

Gnomad4 OTH exome

AF:

0.594

GnomAD4 genome

AF:

0.683

AC:

103828

AN:

152078

Hom.:

36683

Cov.:

AF XY:

0.690

AC XY:

51257

AN XY:

74338

show subpopulations

Gnomad4 AFR

AF:

0.820

Gnomad4 AMR

AF:

0.758

Gnomad4 ASJ

AF:

0.630

Gnomad4 EAS

AF:

0.910

Gnomad4 SAS

AF:

0.795

Gnomad4 FIN

AF:

0.633

Gnomad4 NFE

AF:

0.568

Gnomad4 OTH

AF:

0.695

Alfa

AF:

0.623

Hom.:

3800

Bravo

AF:

0.696

Asia WGS

AF:

0.844

AC:

2929

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

Jun 18, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.2

DANN

Benign

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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