Variant rs77442034 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 0.138 in 657,600 control chromosomes in the GnomAD database, including 7,224 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 0.12 ( 1392 hom., cov: 33)

Exomes 𝑓: 0.14 ( 5832 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.35

Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4

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

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 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:

0.119

AC:

18072

AN:

152140

Hom.:

1388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0318

Gnomad AMI

AF:

0.0428

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.0922

Gnomad EAS

AF:

0.0738

Gnomad SAS

AF:

0.143

Gnomad FIN

AF:

0.168

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.153

Gnomad OTH

AF:

0.102

GnomAD4 exome

AF:

0.144

AC:

72685

AN:

505342

Hom.:

5832

AF XY:

0.143

AC XY:

38423

AN XY:

267758

show subpopulations

Gnomad4 AFR exome

AF:

0.0283

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.0913

Gnomad4 EAS exome

AF:

0.0744

Gnomad4 SAS exome

AF:

0.141

Gnomad4 FIN exome

AF:

0.172

Gnomad4 NFE exome

AF:

0.151

Gnomad4 OTH exome

AF:

0.131

GnomAD4 genome

AF:

0.119

AC:

18089

AN:

152258

Hom.:

1392

Cov.:

AF XY:

0.120

AC XY:

8938

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0317

Gnomad4 AMR

AF:

0.190

Gnomad4 ASJ

AF:

0.0922

Gnomad4 EAS

AF:

0.0739

Gnomad4 SAS

AF:

0.144

Gnomad4 FIN

AF:

0.168

Gnomad4 NFE

AF:

0.153

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.0577

Hom.:

Bravo

AF:

0.115

Asia WGS

AF:

0.107

AC:

373

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

1.0

DANN

Benign

0.85

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