Variant rs978739 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 0.359 in 489,260 control chromosomes in the GnomAD database, including 32,486 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 0.37 ( 10387 hom., cov: 32)

Exomes 𝑓: 0.36 ( 22099 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.592

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=-0.82).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 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:

0.365

AC:

55431

AN:

151806

Hom.:

10376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.323

Gnomad AMR

AF:

0.292

Gnomad ASJ

AF:

0.319

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.454

Gnomad FIN

AF:

0.404

Gnomad MID

AF:

0.392

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.350

GnomAD4 exome

AF:

0.356

AC:

120240

AN:

337336

Hom.:

22099

AF XY:

0.360

AC XY:

62135

AN XY:

172522

show subpopulations

Gnomad4 AFR exome

AF:

0.416

Gnomad4 AMR exome

AF:

0.287

Gnomad4 ASJ exome

AF:

0.319

Gnomad4 EAS exome

AF:

0.342

Gnomad4 SAS exome

AF:

0.468

Gnomad4 FIN exome

AF:

0.380

Gnomad4 NFE exome

AF:

0.350

Gnomad4 OTH exome

AF:

0.353

GnomAD4 genome

AF:

0.365

AC:

55474

AN:

151924

Hom.:

10387

Cov.:

AF XY:

0.366

AC XY:

27147

AN XY:

74248

show subpopulations

Gnomad4 AFR

AF:

0.400

Gnomad4 AMR

AF:

0.292

Gnomad4 ASJ

AF:

0.319

Gnomad4 EAS

AF:

0.340

Gnomad4 SAS

AF:

0.455

Gnomad4 FIN

AF:

0.404

Gnomad4 NFE

AF:

0.353

Gnomad4 OTH

AF:

0.355

Alfa

AF:

0.269

Hom.:

988

Bravo

AF:

0.356

Asia WGS

AF:

0.417

AC:

1449

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.1

DANN

Benign

0.80

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