Variant chr2-203879078-T-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 0.38 in 152,066 control chromosomes in the GnomAD database, including 11,470 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 0.38 ( 11470 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.05

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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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:

0.380

AC:

57735

AN:

151948

Hom.:

11450

Cov.:

show subpopulations

Gnomad AFR

AF:

0.415

Gnomad AMI

AF:

0.378

Gnomad AMR

AF:

0.392

Gnomad ASJ

AF:

0.257

Gnomad EAS

AF:

0.591

Gnomad SAS

AF:

0.285

Gnomad FIN

AF:

0.503

Gnomad MID

AF:

0.207

Gnomad NFE

AF:

0.336

Gnomad OTH

AF:

0.330

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

GnomAD4 genome

AF:

0.380

AC:

57805

AN:

152066

Hom.:

11470

Cov.:

AF XY:

0.387

AC XY:

28785

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.415

Gnomad4 AMR

AF:

0.393

Gnomad4 ASJ

AF:

0.257

Gnomad4 EAS

AF:

0.590

Gnomad4 SAS

AF:

0.285

Gnomad4 FIN

AF:

0.503

Gnomad4 NFE

AF:

0.336

Gnomad4 OTH

AF:

0.329

Alfa

AF:

0.367

Hom.:

1271

Bravo

AF:

0.377

Asia WGS

AF:

0.403

AC:

1397

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.027

DANN

Benign

0.36

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