Variant chr2-118541311-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 0.501 in 152,084 control chromosomes in the GnomAD database, including 19,496 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 0.50 ( 19496 hom., cov: 33)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91

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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 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:

0.501

AC:

76162

AN:

151966

Hom.:

19469

Cov.:

show subpopulations

Gnomad AFR

AF:

0.608

Gnomad AMI

AF:

0.596

Gnomad AMR

AF:

0.516

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.394

Gnomad SAS

AF:

0.349

Gnomad FIN

AF:

0.467

Gnomad MID

AF:

0.399

Gnomad NFE

AF:

0.462

Gnomad OTH

AF:

0.486

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

GnomAD4 genome

AF:

0.501

AC:

76238

AN:

152084

Hom.:

19496

Cov.:

AF XY:

0.497

AC XY:

36947

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.608

Gnomad4 AMR

AF:

0.517

Gnomad4 ASJ

AF:

0.398

Gnomad4 EAS

AF:

0.394

Gnomad4 SAS

AF:

0.349

Gnomad4 FIN

AF:

0.467

Gnomad4 NFE

AF:

0.462

Gnomad4 OTH

AF:

0.482

Alfa

AF:

0.463

Hom.:

33296

Bravo

AF:

0.512

Asia WGS

AF:

0.381

AC:

1325

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.031

DANN

Benign

0.44

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