20-61014216-C-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 0.321 in 152,014 control chromosomes in the GnomAD database, including 8,095 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 0.32 ( 8095 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.719
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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.479 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:
0.321
AC:
48746
AN:
151896
Hom.:
8099
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.249
Gnomad AMI
AF:
0.251
Gnomad AMR
AF:
0.386
Gnomad ASJ
AF:
0.366
Gnomad EAS
AF:
0.471
Gnomad SAS
AF:
0.495
Gnomad FIN
AF:
0.301
Gnomad MID
AF:
0.389
Gnomad NFE
AF:
0.327
Gnomad OTH
AF:
0.339
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.321
AC:
48759
AN:
152014
Hom.:
8095
Cov.:
32
AF XY:
0.325
AC XY:
24116
AN XY:
74296
show subpopulations
Gnomad4 AFR
AF:
0.249
Gnomad4 AMR
AF:
0.385
Gnomad4 ASJ
AF:
0.366
Gnomad4 EAS
AF:
0.471
Gnomad4 SAS
AF:
0.495
Gnomad4 FIN
AF:
0.301
Gnomad4 NFE
AF:
0.327
Gnomad4 OTH
AF:
0.338
Alfa
AF:
0.341
Hom.:
18370
Bravo
AF:
0.327
Asia WGS
AF:
0.446
AC:
1549
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.88
DANN
Benign
0.77

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: rs6129005; hg19: chr20-59589272; API