rs41526846

Variant summary

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

The ENST00000794040.1(ENSG00000303377):​n.194-1648C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0265 in 152,202 control chromosomes in the GnomAD database, including 193 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 0.026 ( 193 hom., cov: 32)

Consequence

ENSG00000303377
ENST00000794040.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.685

Publications

1 publications found
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=-0.91).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105378515XR_001747605.1 linkn.703-1648C>T intron_variant Intron 6 of 6
LOC105378515XR_001747606.1 linkn.993+3978C>T intron_variant Intron 7 of 7

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000303377ENST00000794040.1 linkn.194-1648C>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.0264
AC:
4022
AN:
152090
Hom.:
192
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00522
Gnomad AMI
AF:
0.0307
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.0115
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0176
Gnomad FIN
AF:
0.0512
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0175
Gnomad OTH
AF:
0.0234
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0265
AC:
4029
AN:
152202
Hom.:
193
Cov.:
32
AF XY:
0.0294
AC XY:
2187
AN XY:
74416
show subpopulations
African (AFR)
AF:
0.00520
AC:
216
AN:
41512
American (AMR)
AF:
0.122
AC:
1874
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
0.0115
AC:
40
AN:
3468
East Asian (EAS)
AF:
0.00
AC:
0
AN:
5178
South Asian (SAS)
AF:
0.0178
AC:
86
AN:
4826
European-Finnish (FIN)
AF:
0.0512
AC:
542
AN:
10584
Middle Eastern (MID)
AF:
0.00340
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
0.0175
AC:
1193
AN:
68010
Other (OTH)
AF:
0.0232
AC:
49
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
190
380
570
760
950
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
42
84
126
168
210
<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:
0.0164
Hom.:
12
Bravo
AF:
0.0314
Asia WGS
AF:
0.0140
AC:
49
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.96
DANN
Benign
0.60
PhyloP100
-0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs41526846; hg19: chr10-122051957; API