Variant 18-49560628-A-C 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 0.824 in 152,260 control chromosomes in the GnomAD database, including 52,628 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 0.82 ( 52618 hom., cov: 33)

Exomes 𝑓: 0.91 ( 10 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.800

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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 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:

0.824

AC:

125320

AN:

152120

Hom.:

52566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.956

Gnomad AMI

AF:

0.840

Gnomad AMR

AF:

0.665

Gnomad ASJ

AF:

0.877

Gnomad EAS

AF:

0.548

Gnomad SAS

AF:

0.831

Gnomad FIN

AF:

0.729

Gnomad MID

AF:

0.933

Gnomad NFE

AF:

0.810

Gnomad OTH

AF:

0.842

GnomAD4 exome

AF:

0.909

AC:

AN:

Hom.:

AF XY:

0.833

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

1.00

Gnomad4 NFE exome

AF:

0.857

GnomAD4 genome

AF:

0.824

AC:

125422

AN:

152238

Hom.:

52618

Cov.:

AF XY:

0.818

AC XY:

60842

AN XY:

74414

show subpopulations

Gnomad4 AFR

AF:

0.957

Gnomad4 AMR

AF:

0.664

Gnomad4 ASJ

AF:

0.877

Gnomad4 EAS

AF:

0.548

Gnomad4 SAS

AF:

0.830

Gnomad4 FIN

AF:

0.729

Gnomad4 NFE

AF:

0.810

Gnomad4 OTH

AF:

0.844

Alfa

AF:

0.814

Hom.:

79493

Bravo

AF:

0.821

Asia WGS

AF:

0.723

AC:

2513

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

8.6

DANN

Benign

0.35

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