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rs2240191

Variant summary

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

The NM_001143854.2(RPH3A):c.*1146G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,200 control chromosomes in the GnomAD database, including 6,230 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 0.26 ( 6230 hom., cov: 32)
Exomes 𝑓: 0.17 ( 0 hom. )

Consequence

RPH3A
NM_001143854.2 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.24
Variant links:
Genes affected
RPH3A (HGNC:17056): (rabphilin 3A) The protein encoded by this gene is thought to be an effector for RAB3A, which is a small G protein that acts in the late stages of neurotransmitter exocytosis. The encoded protein may be involved in neurotransmitter release and synaptic vesicle traffic. [provided by RefSeq, Dec 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RPH3ANM_001143854.2 linkuse as main transcriptc.*1146G>T 3_prime_UTR_variant 22/22 ENST00000389385.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RPH3AENST00000389385.9 linkuse as main transcriptc.*1146G>T 3_prime_UTR_variant 22/221 NM_001143854.2 P3Q9Y2J0-1
RPH3AENST00000549913.6 linkuse as main transcriptn.4233G>T non_coding_transcript_exon_variant 14/141
RPH3AENST00000415485.7 linkuse as main transcriptc.*1146G>T 3_prime_UTR_variant 21/215 P3Q9Y2J0-1
RPH3AENST00000549324.1 linkuse as main transcriptn.1738G>T non_coding_transcript_exon_variant 2/24

Frequencies

GnomAD3 genomes
AF:
0.263
AC:
40008
AN:
151956
Hom.:
6216
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.411
Gnomad AMI
AF:
0.0943
Gnomad AMR
AF:
0.317
Gnomad ASJ
AF:
0.216
Gnomad EAS
AF:
0.445
Gnomad SAS
AF:
0.196
Gnomad FIN
AF:
0.152
Gnomad MID
AF:
0.247
Gnomad NFE
AF:
0.174
Gnomad OTH
AF:
0.272
GnomAD4 exome
AF:
0.175
AC:
22
AN:
126
Hom.:
0
Cov.:
0
AF XY:
0.149
AC XY:
14
AN XY:
94
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.170
Gnomad4 OTH exome
AF:
0.125
GnomAD4 genome
AF:
0.263
AC:
40071
AN:
152074
Hom.:
6230
Cov.:
32
AF XY:
0.262
AC XY:
19450
AN XY:
74338
show subpopulations
Gnomad4 AFR
AF:
0.411
Gnomad4 AMR
AF:
0.317
Gnomad4 ASJ
AF:
0.216
Gnomad4 EAS
AF:
0.445
Gnomad4 SAS
AF:
0.196
Gnomad4 FIN
AF:
0.152
Gnomad4 NFE
AF:
0.174
Gnomad4 OTH
AF:
0.272
Alfa
AF:
0.200
Hom.:
4443
Bravo
AF:
0.288
Asia WGS
AF:
0.306
AC:
1063
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
Cadd
Benign
0.15
Dann
Benign
0.78

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: rs2240191; hg19: chr12-113335731; API