Variant 2-75598693-G-A 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 0.553 in 152,098 control chromosomes in the GnomAD database, including 23,420 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 0.55 ( 23407 hom., cov: 32)

Exomes 𝑓: 0.52 ( 13 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.557

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=-0.61).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.588 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:

0.553

AC:

84006

AN:

151890

Hom.:

23378

Cov.:

show subpopulations

Gnomad AFR

AF:

0.594

Gnomad AMI

AF:

0.442

Gnomad AMR

AF:

0.575

Gnomad ASJ

AF:

0.385

Gnomad EAS

AF:

0.592

Gnomad SAS

AF:

0.591

Gnomad FIN

AF:

0.572

Gnomad MID

AF:

0.503

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.555

GnomAD4 exome

AF:

0.522

AC:

AN:

Hom.:

AF XY:

0.533

AC XY:

AN XY:

show subpopulations

Gnomad4 ASJ exome

AF:

0.500

Gnomad4 SAS exome

AF:

1.00

Gnomad4 FIN exome

AF:

0.700

Gnomad4 NFE exome

AF:

0.548

Gnomad4 OTH exome

AF:

0.214

GnomAD4 genome

AF:

0.553

AC:

84098

AN:

152008

Hom.:

23407

Cov.:

AF XY:

0.556

AC XY:

41330

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.595

Gnomad4 AMR

AF:

0.575

Gnomad4 ASJ

AF:

0.385

Gnomad4 EAS

AF:

0.592

Gnomad4 SAS

AF:

0.590

Gnomad4 FIN

AF:

0.572

Gnomad4 NFE

AF:

0.525

Gnomad4 OTH

AF:

0.555

Alfa

AF:

0.529

Hom.:

43807

Bravo

AF:

0.552

Asia WGS

AF:

0.644

AC:

2242

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

9.3

DANN

Benign

0.75

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