rs216416

Variant summary

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

The NR_015341.2(SMURF2P1-LRRC37BP1):​n.519+65G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 979,550 control chromosomes in the GnomAD database, including 10,658 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 0.17 ( 2685 hom., cov: 30)
Exomes 𝑓: 0.13 ( 7973 hom. )

Consequence

SMURF2P1-LRRC37BP1
NR_015341.2 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.546
Variant links:
Genes affected
SMURF2P1 (HGNC:44402): (SMAD specific E3 ubiquitin protein ligase 2 pseudogene 1)

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=-0.75).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SMURF2P1-LRRC37BP1NR_015341.2 linkuse as main transcriptn.519+65G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SMURF2P1ENST00000514992.2 linkuse as main transcriptn.342+65G>A intron_variant, non_coding_transcript_variant
ENST00000579301.5 linkuse as main transcriptn.431+65G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.173
AC:
25839
AN:
149446
Hom.:
2670
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.295
Gnomad AMI
AF:
0.129
Gnomad AMR
AF:
0.184
Gnomad ASJ
AF:
0.126
Gnomad EAS
AF:
0.127
Gnomad SAS
AF:
0.195
Gnomad FIN
AF:
0.0867
Gnomad MID
AF:
0.141
Gnomad NFE
AF:
0.116
Gnomad OTH
AF:
0.163
GnomAD4 exome
AF:
0.131
AC:
109124
AN:
829988
Hom.:
7973
AF XY:
0.131
AC XY:
54264
AN XY:
413040
show subpopulations
Gnomad4 AFR exome
AF:
0.301
Gnomad4 AMR exome
AF:
0.174
Gnomad4 ASJ exome
AF:
0.130
Gnomad4 EAS exome
AF:
0.156
Gnomad4 SAS exome
AF:
0.180
Gnomad4 FIN exome
AF:
0.0872
Gnomad4 NFE exome
AF:
0.122
Gnomad4 OTH exome
AF:
0.143
GnomAD4 genome
AF:
0.173
AC:
25895
AN:
149562
Hom.:
2685
Cov.:
30
AF XY:
0.171
AC XY:
12478
AN XY:
72936
show subpopulations
Gnomad4 AFR
AF:
0.295
Gnomad4 AMR
AF:
0.184
Gnomad4 ASJ
AF:
0.126
Gnomad4 EAS
AF:
0.127
Gnomad4 SAS
AF:
0.197
Gnomad4 FIN
AF:
0.0867
Gnomad4 NFE
AF:
0.116
Gnomad4 OTH
AF:
0.161
Alfa
AF:
0.142
Hom.:
200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
1.5
DANN
Benign
0.58
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs216416; hg19: chr17-28935645; API