Variant chr18-50872497-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 0.321 in 152,028 control chromosomes in the GnomAD database, including 8,148 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 0.32 ( 8148 hom., cov: 32)

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.677

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=-0.99).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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:

0.321

AC:

48784

AN:

151910

Hom.:

8143

Cov.:

show subpopulations

Gnomad AFR

AF:

0.246

Gnomad AMI

AF:

0.542

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.335

Gnomad EAS

AF:

0.332

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.432

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.372

Gnomad OTH

AF:

0.304

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

GnomAD4 genome

AF:

0.321

AC:

48810

AN:

152028

Hom.:

8148

Cov.:

AF XY:

0.319

AC XY:

23686

AN XY:

74318

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.245

Gnomad4 ASJ

AF:

0.335

Gnomad4 EAS

AF:

0.332

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.432

Gnomad4 NFE

AF:

0.372

Gnomad4 OTH

AF:

0.309

Alfa

AF:

0.344

Hom.:

1167

Bravo

AF:

0.309

Asia WGS

AF:

0.274

AC:

953

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

6.6

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