rs605066

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000647815.1(ENSG00000226571):​n.134+21914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,802 control chromosomes in the GnomAD database, including 22,164 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 0.53 ( 22164 hom., cov: 32)

Consequence

ENSG00000226571
ENST00000647815.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0880
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.678 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000226571ENST00000647815.1 linkn.134+21914C>T intron_variant Intron 1 of 2

Frequencies

GnomAD3 genomes
AF:
0.534
AC:
81039
AN:
151684
Hom.:
22142
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.442
Gnomad AMI
AF:
0.586
Gnomad AMR
AF:
0.567
Gnomad ASJ
AF:
0.639
Gnomad EAS
AF:
0.307
Gnomad SAS
AF:
0.696
Gnomad FIN
AF:
0.493
Gnomad MID
AF:
0.580
Gnomad NFE
AF:
0.588
Gnomad OTH
AF:
0.561
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.534
AC:
81091
AN:
151802
Hom.:
22164
Cov.:
32
AF XY:
0.533
AC XY:
39542
AN XY:
74162
show subpopulations
Gnomad4 AFR
AF:
0.441
AC:
0.441374
AN:
0.441374
Gnomad4 AMR
AF:
0.567
AC:
0.566881
AN:
0.566881
Gnomad4 ASJ
AF:
0.639
AC:
0.638825
AN:
0.638825
Gnomad4 EAS
AF:
0.307
AC:
0.307231
AN:
0.307231
Gnomad4 SAS
AF:
0.698
AC:
0.697718
AN:
0.697718
Gnomad4 FIN
AF:
0.493
AC:
0.492954
AN:
0.492954
Gnomad4 NFE
AF:
0.588
AC:
0.588345
AN:
0.588345
Gnomad4 OTH
AF:
0.556
AC:
0.55619
AN:
0.55619
Heterozygous variant carriers
0
1851
3701
5552
7402
9253
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
706
1412
2118
2824
3530
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.560
Hom.:
54931
Bravo
AF:
0.529
Asia WGS
AF:
0.514
AC:
1787
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.47
DANN
Benign
0.17

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: rs605066; hg19: chr6-139829666; API