16-78019746-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000563114.1(ENSG00000261540):​n.42-4617T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,082 control chromosomes in the GnomAD database, including 32,464 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 0.63 ( 32464 hom., cov: 32)

Consequence

ENSG00000261540
ENST00000563114.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.146
Variant links:
Genes affected

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=-1.0).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.767 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
ENSG00000261540ENST00000563114.1 linkn.42-4617T>A intron_variant 1

Frequencies

GnomAD3 genomes
AF:
0.630
AC:
95697
AN:
151964
Hom.:
32448
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.355
Gnomad AMI
AF:
0.825
Gnomad AMR
AF:
0.692
Gnomad ASJ
AF:
0.678
Gnomad EAS
AF:
0.692
Gnomad SAS
AF:
0.788
Gnomad FIN
AF:
0.781
Gnomad MID
AF:
0.669
Gnomad NFE
AF:
0.737
Gnomad OTH
AF:
0.664
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.630
AC:
95747
AN:
152082
Hom.:
32464
Cov.:
32
AF XY:
0.635
AC XY:
47238
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.355
Gnomad4 AMR
AF:
0.692
Gnomad4 ASJ
AF:
0.678
Gnomad4 EAS
AF:
0.691
Gnomad4 SAS
AF:
0.788
Gnomad4 FIN
AF:
0.781
Gnomad4 NFE
AF:
0.737
Gnomad4 OTH
AF:
0.667
Alfa
AF:
0.574
Hom.:
1891
Bravo
AF:
0.610
Asia WGS
AF:
0.740
AC:
2568
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
0.97
DANN
Benign
0.13

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: rs2735413; hg19: chr16-78053643; API