rs6610650

Variant summary

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

The ENST00000465127.1(ENSG00000250349):​c.171+351261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 110,416 control chromosomes in the GnomAD database, including 3,985 homozygotes. There are 8,314 hemizygotes in GnomAD. 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 0.27 ( 3985 hom., 8314 hem., cov: 22)

Consequence

ENSG00000250349
ENST00000465127.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.200

Publications

8 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 (AFR) allele frequency at 95% confidence interval = 0.533 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
ENSG00000250349ENST00000465127.1 linkc.171+351261G>A intron_variant Intron 3 of 8 5 ENSP00000417050.1 B4E171

Frequencies

GnomAD3 genomes
AF:
0.267
AC:
29436
AN:
110369
Hom.:
3979
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.539
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.216
Gnomad ASJ
AF:
0.204
Gnomad EAS
AF:
0.0699
Gnomad SAS
AF:
0.190
Gnomad FIN
AF:
0.123
Gnomad MID
AF:
0.0987
Gnomad NFE
AF:
0.161
Gnomad OTH
AF:
0.215
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.267
AC:
29485
AN:
110416
Hom.:
3985
Cov.:
22
AF XY:
0.254
AC XY:
8314
AN XY:
32750
show subpopulations
African (AFR)
AF:
0.540
AC:
16305
AN:
30208
American (AMR)
AF:
0.216
AC:
2254
AN:
10453
Ashkenazi Jewish (ASJ)
AF:
0.204
AC:
535
AN:
2627
East Asian (EAS)
AF:
0.0693
AC:
244
AN:
3522
South Asian (SAS)
AF:
0.191
AC:
502
AN:
2625
European-Finnish (FIN)
AF:
0.123
AC:
716
AN:
5831
Middle Eastern (MID)
AF:
0.0948
AC:
20
AN:
211
European-Non Finnish (NFE)
AF:
0.161
AC:
8512
AN:
52756
Other (OTH)
AF:
0.218
AC:
328
AN:
1502
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
665
1330
1994
2659
3324
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
286
572
858
1144
1430
<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:
0.223
Hom.:
11637
Bravo
AF:
0.288

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.54
DANN
Benign
0.39
PhyloP100
0.20

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs6610650; hg19: chrX-37636514; API