19-49255975-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 0.496 in 152,132 control chromosomes in the GnomAD database, including 18,901 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 ( 18865 hom., cov: 31)
Exomes 𝑓: 0.51 ( 36 hom. )

Consequence

SLC6A21P
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.63
Variant links:
Genes affected
SLC6A21P (HGNC:31400): (solute carrier family 6 member 21, pseudogene)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLC6A21P n.49255975G>T intragenic_variant
LOC107985340XR_001753971.2 linkn.467-13428G>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLC6A21PENST00000599458.1 linkn.91+37C>A intron_variant 6

Frequencies

GnomAD3 genomes
AF:
0.496
AC:
75314
AN:
151782
Hom.:
18854
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.435
Gnomad AMI
AF:
0.593
Gnomad AMR
AF:
0.569
Gnomad ASJ
AF:
0.555
Gnomad EAS
AF:
0.627
Gnomad SAS
AF:
0.590
Gnomad FIN
AF:
0.511
Gnomad MID
AF:
0.503
Gnomad NFE
AF:
0.494
Gnomad OTH
AF:
0.502
GnomAD4 exome
AF:
0.509
AC:
118
AN:
232
Hom.:
36
Cov.:
0
AF XY:
0.520
AC XY:
79
AN XY:
152
show subpopulations
Gnomad4 AMR exome
AF:
0.500
Gnomad4 ASJ exome
AF:
0.750
Gnomad4 EAS exome
AF:
1.00
Gnomad4 FIN exome
AF:
0.489
Gnomad4 NFE exome
AF:
0.483
Gnomad4 OTH exome
AF:
0.750
GnomAD4 genome
AF:
0.496
AC:
75363
AN:
151900
Hom.:
18865
Cov.:
31
AF XY:
0.503
AC XY:
37334
AN XY:
74226
show subpopulations
Gnomad4 AFR
AF:
0.434
Gnomad4 AMR
AF:
0.570
Gnomad4 ASJ
AF:
0.555
Gnomad4 EAS
AF:
0.627
Gnomad4 SAS
AF:
0.590
Gnomad4 FIN
AF:
0.511
Gnomad4 NFE
AF:
0.494
Gnomad4 OTH
AF:
0.501
Alfa
AF:
0.448
Hom.:
3410
Bravo
AF:
0.497

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.075
DANN
Benign
0.60

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: rs352822; hg19: chr19-49759232; API