Variant 19-48758444-C-T 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 0.0717 in 409,302 control chromosomes in the GnomAD database, including 2,801 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 0.072 ( 640 hom., cov: 31)

Exomes 𝑓: 0.071 ( 2161 hom. )

Consequence

Unknown

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.740

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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 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:

0.0723

AC:

10855

AN:

150144

Hom.:

637

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.0752

Gnomad AMR

AF:

0.0898

Gnomad ASJ

AF:

0.0254

Gnomad EAS

AF:

0.277

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.0273

Gnomad MID

AF:

0.0350

Gnomad NFE

AF:

0.0335

Gnomad OTH

AF:

0.0611

GnomAD4 exome

AF:

0.0713

AC:

18462

AN:

259054

Hom.:

2161

AF XY:

0.0698

AC XY:

9254

AN XY:

132650

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.0931

Gnomad4 ASJ exome

AF:

0.0203

Gnomad4 EAS exome

AF:

0.408

Gnomad4 SAS exome

AF:

0.108

Gnomad4 FIN exome

AF:

0.0231

Gnomad4 NFE exome

AF:

0.0326

Gnomad4 OTH exome

AF:

0.0586

GnomAD4 genome

AF:

0.0724

AC:

10876

AN:

150248

Hom.:

640

Cov.:

AF XY:

0.0746

AC XY:

5469

AN XY:

73356

show subpopulations

Gnomad4 AFR

AF:

0.117

Gnomad4 AMR

AF:

0.0898

Gnomad4 ASJ

AF:

0.0254

Gnomad4 EAS

AF:

0.277

Gnomad4 SAS

AF:

0.116

Gnomad4 FIN

AF:

0.0273

Gnomad4 NFE

AF:

0.0335

Gnomad4 OTH

AF:

0.0614

Alfa

AF:

0.0572

Hom.:

Bravo

AF:

0.0796

Asia WGS

AF:

0.205

AC:

710

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

6.4

DANN

Benign

0.82

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