GeneBe

rs17103265

Positions:

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The variant allele was found at a frequency of 0.0197 in 152,254 control chromosomes in the GnomAD database, including 121 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 121 hom., cov: 30)

Consequence


intergenic_region

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.14
Variant links:
Genes affected

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 14-35405502-GA-G is Benign according to our data. Variant chr14-35405502-GA-G is described in ClinVar as [Benign]. Clinvar id is 1168279.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.35405503delA intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.0197
AC:
2995
AN:
152136
Hom.:
121
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.0280
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0109
Gnomad ASJ
AF:
0.00144
Gnomad EAS
AF:
0.176
Gnomad SAS
AF:
0.0716
Gnomad FIN
AF:
0.0237
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.00153
Gnomad OTH
AF:
0.0201
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0197
AC:
2997
AN:
152254
Hom.:
121
Cov.:
30
AF XY:
0.0228
AC XY:
1694
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0281
Gnomad4 AMR
AF:
0.0109
Gnomad4 ASJ
AF:
0.00144
Gnomad4 EAS
AF:
0.175
Gnomad4 SAS
AF:
0.0713
Gnomad4 FIN
AF:
0.0237
Gnomad4 NFE
AF:
0.00153
Gnomad4 OTH
AF:
0.0209
Alfa
AF:
0.00967
Hom.:
5
Bravo
AF:
0.0191
Asia WGS
AF:
0.145
AC:
504
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Ectodermal dysplasia and immunodeficiency 2 Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 04, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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: rs17103265; hg19: chr14-35874708; API