Variant chr7-133217043-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The variant allele was found at a frequency of 0.487 in 152,102 control chromosomes in the GnomAD database, including 21,722 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 0.49 ( 21722 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.49

Variant links:

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ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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:

0.487

AC:

73945

AN:

151982

Hom.:

21675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.831

Gnomad AMI

AF:

0.282

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.581

Gnomad SAS

AF:

0.499

Gnomad FIN

AF:

0.306

Gnomad MID

AF:

0.436

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.464

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

GnomAD4 genome

AF:

0.487

AC:

74044

AN:

152102

Hom.:

21722

Cov.:

AF XY:

0.483

AC XY:

35913

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.831

Gnomad4 AMR

AF:

0.334

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.581

Gnomad4 SAS

AF:

0.498

Gnomad4 FIN

AF:

0.306

Gnomad4 NFE

AF:

0.340

Gnomad4 OTH

AF:

0.470

Alfa

AF:

0.445

Hom.:

3471

Bravo

AF:

0.500

Asia WGS

AF:

0.547

AC:

1901

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

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