19-48758426-G-T

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 0.0965 in 454,270 control chromosomes in the GnomAD database, including 5,483 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 0.13 ( 2630 hom., cov: 31)
Exomes 𝑓: 0.079 ( 2853 hom. )

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.85
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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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:
0.132
AC:
19998
AN:
151558
Hom.:
2609
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.324
Gnomad AMI
AF:
0.0757
Gnomad AMR
AF:
0.111
Gnomad ASJ
AF:
0.0272
Gnomad EAS
AF:
0.275
Gnomad SAS
AF:
0.117
Gnomad FIN
AF:
0.0277
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0343
Gnomad OTH
AF:
0.0993
GnomAD4 exome
AF:
0.0785
AC:
23760
AN:
302602
Hom.:
2853
AF XY:
0.0763
AC XY:
11879
AN XY:
155634
show subpopulations
Gnomad4 AFR exome
AF:
0.327
Gnomad4 AMR exome
AF:
0.119
Gnomad4 ASJ exome
AF:
0.0222
Gnomad4 EAS exome
AF:
0.407
Gnomad4 SAS exome
AF:
0.121
Gnomad4 FIN exome
AF:
0.0245
Gnomad4 NFE exome
AF:
0.0349
Gnomad4 OTH exome
AF:
0.0788
GnomAD4 genome
AF:
0.132
AC:
20058
AN:
151668
Hom.:
2630
Cov.:
31
AF XY:
0.133
AC XY:
9850
AN XY:
74126
show subpopulations
Gnomad4 AFR
AF:
0.324
Gnomad4 AMR
AF:
0.111
Gnomad4 ASJ
AF:
0.0272
Gnomad4 EAS
AF:
0.274
Gnomad4 SAS
AF:
0.117
Gnomad4 FIN
AF:
0.0277
Gnomad4 NFE
AF:
0.0343
Gnomad4 OTH
AF:
0.0992
Alfa
AF:
0.0171
Hom.:
10
Bravo
AF:
0.149
Asia WGS
AF:
0.222
AC:
770
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.13
DANN
Benign
0.54

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.

Other links and lift over

dbSNP: rs11665896; hg19: chr19-49261683; API