Variant rs753013 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 0.424 in 151,956 control chromosomes in the GnomAD database, including 14,487 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 0.42 ( 14487 hom., cov: 31)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.597

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=-0.93).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64479

AN:

151838

Hom.:

14477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.436

Gnomad AMR

AF:

0.578

Gnomad ASJ

AF:

0.474

Gnomad EAS

AF:

0.340

Gnomad SAS

AF:

0.488

Gnomad FIN

AF:

0.510

Gnomad MID

AF:

0.369

Gnomad NFE

AF:

0.455

Gnomad OTH

AF:

0.423

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

GnomAD4 genome

AF:

0.424

AC:

64503

AN:

151956

Hom.:

14487

Cov.:

AF XY:

0.430

AC XY:

31962

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.296

Gnomad4 AMR

AF:

0.579

Gnomad4 ASJ

AF:

0.474

Gnomad4 EAS

AF:

0.341

Gnomad4 SAS

AF:

0.487

Gnomad4 FIN

AF:

0.510

Gnomad4 NFE

AF:

0.455

Gnomad4 OTH

AF:

0.418

Alfa

AF:

0.430

Hom.:

1775

Bravo

AF:

0.424

Asia WGS

AF:

0.415

AC:

1441

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.5

DANN

Benign

0.66

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