rs2305491

Positions:

Variant summary

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

The NM_003310.5(EIPR1):​c.654-238G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.861 in 367,636 control chromosomes in the GnomAD database, including 138,235 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 0.86 ( 56580 hom., cov: 30)
Exomes 𝑓: 0.86 ( 81655 hom. )

Consequence

EIPR1
NM_003310.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.446
Variant links:
Genes affected
EIPR1 (HGNC:12383): (EARP complex and GARP complex interacting protein 1) This gene has been reported in PMID 9403053 as one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. Alignment of this gene to genomic sequence data suggests that this gene resides on chromosome 2 rather than chromosome 11. [provided by RefSeq, Dec 2008]

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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
EIPR1NM_003310.5 linkuse as main transcriptc.654-238G>A intron_variant ENST00000382125.9 NP_003301.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
EIPR1ENST00000382125.9 linkuse as main transcriptc.654-238G>A intron_variant 1 NM_003310.5 ENSP00000371559 P1

Frequencies

GnomAD3 genomes
AF:
0.859
AC:
130454
AN:
151932
Hom.:
56544
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.813
Gnomad AMI
AF:
0.961
Gnomad AMR
AF:
0.889
Gnomad ASJ
AF:
0.930
Gnomad EAS
AF:
0.492
Gnomad SAS
AF:
0.772
Gnomad FIN
AF:
0.855
Gnomad MID
AF:
0.915
Gnomad NFE
AF:
0.908
Gnomad OTH
AF:
0.876
GnomAD4 exome
AF:
0.863
AC:
186028
AN:
215586
Hom.:
81655
Cov.:
4
AF XY:
0.863
AC XY:
94931
AN XY:
109948
show subpopulations
Gnomad4 AFR exome
AF:
0.813
Gnomad4 AMR exome
AF:
0.900
Gnomad4 ASJ exome
AF:
0.930
Gnomad4 EAS exome
AF:
0.514
Gnomad4 SAS exome
AF:
0.780
Gnomad4 FIN exome
AF:
0.869
Gnomad4 NFE exome
AF:
0.911
Gnomad4 OTH exome
AF:
0.866
GnomAD4 genome
AF:
0.859
AC:
130551
AN:
152050
Hom.:
56580
Cov.:
30
AF XY:
0.854
AC XY:
63493
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.813
Gnomad4 AMR
AF:
0.889
Gnomad4 ASJ
AF:
0.930
Gnomad4 EAS
AF:
0.492
Gnomad4 SAS
AF:
0.774
Gnomad4 FIN
AF:
0.855
Gnomad4 NFE
AF:
0.908
Gnomad4 OTH
AF:
0.877
Alfa
AF:
0.896
Hom.:
32268
Bravo
AF:
0.860
Asia WGS
AF:
0.633
AC:
2206
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.19
DANN
Benign
0.64

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: rs2305491; hg19: chr2-3198175; API