15-56090097-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022841.7(RFX7):​c.*3248T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,174 control chromosomes in the GnomAD database, including 1,660 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 0.12 ( 1660 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

RFX7
NM_022841.7 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.75
Variant links:
Genes affected
RFX7 (HGNC:25777): (regulatory factor X7) RFX7 is a member of the regulatory factor X (RFX) family of transcription factors (see RFX1, MIM 600006) (Aftab et al., 2008 [PubMed 18673564]).[supplied by OMIM, Mar 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RFX7NM_022841.7 linkuse as main transcriptc.*3248T>C 3_prime_UTR_variant 10/10 ENST00000559447.8 NP_073752.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RFX7ENST00000559447.8 linkuse as main transcriptc.*3248T>C 3_prime_UTR_variant 10/105 NM_022841.7 ENSP00000453281 P1Q2KHR2-3

Frequencies

GnomAD3 genomes
AF:
0.123
AC:
18769
AN:
152056
Hom.:
1660
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0857
Gnomad AMI
AF:
0.101
Gnomad AMR
AF:
0.133
Gnomad ASJ
AF:
0.202
Gnomad EAS
AF:
0.492
Gnomad SAS
AF:
0.308
Gnomad FIN
AF:
0.0684
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.156
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
2
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.123
AC:
18785
AN:
152174
Hom.:
1660
Cov.:
32
AF XY:
0.127
AC XY:
9470
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.0857
Gnomad4 AMR
AF:
0.133
Gnomad4 ASJ
AF:
0.202
Gnomad4 EAS
AF:
0.493
Gnomad4 SAS
AF:
0.308
Gnomad4 FIN
AF:
0.0684
Gnomad4 NFE
AF:
0.107
Gnomad4 OTH
AF:
0.158
Alfa
AF:
0.116
Hom.:
1062
Bravo
AF:
0.126
Asia WGS
AF:
0.333
AC:
1161
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.67
CADD
Benign
11
DANN
Benign
0.86

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16976734; hg19: chr15-56382295; API