rs11176419

Variant summary

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

The NM_001379345.1(GRIP1):​c.133+36186A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0813 in 152,234 control chromosomes in the GnomAD database, including 640 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 0.081 ( 640 hom., cov: 32)

Consequence

GRIP1
NM_001379345.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.276
Variant links:
Genes affected
GRIP1 (HGNC:18708): (glutamate receptor interacting protein 1) This gene encodes a member of the glutamate receptor interacting protein family. The encoded scaffold protein binds to and mediates the trafficking and membrane organization of a number of transmembrane proteins. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, May 2010]

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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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRIP1NM_001366723.1 linkuse as main transcriptc.133+36186A>G intron_variant
GRIP1NM_001366724.1 linkuse as main transcriptc.133+36186A>G intron_variant
GRIP1NM_001379345.1 linkuse as main transcriptc.133+36186A>G intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRIP1ENST00000538373.1 linkuse as main transcriptc.-420+36186A>G intron_variant 4
GRIP1ENST00000539540.5 linkuse as main transcriptc.-114+36065A>G intron_variant 5
GRIP1ENST00000540433.5 linkuse as main transcriptc.-33+36065A>G intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.0812
AC:
12357
AN:
152116
Hom.:
633
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0887
Gnomad AMI
AF:
0.164
Gnomad AMR
AF:
0.159
Gnomad ASJ
AF:
0.0995
Gnomad EAS
AF:
0.119
Gnomad SAS
AF:
0.147
Gnomad FIN
AF:
0.0106
Gnomad MID
AF:
0.127
Gnomad NFE
AF:
0.0598
Gnomad OTH
AF:
0.101
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0813
AC:
12377
AN:
152234
Hom.:
640
Cov.:
32
AF XY:
0.0812
AC XY:
6047
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0888
Gnomad4 AMR
AF:
0.160
Gnomad4 ASJ
AF:
0.0995
Gnomad4 EAS
AF:
0.118
Gnomad4 SAS
AF:
0.147
Gnomad4 FIN
AF:
0.0106
Gnomad4 NFE
AF:
0.0598
Gnomad4 OTH
AF:
0.100
Alfa
AF:
0.0709
Hom.:
557
Bravo
AF:
0.0952
Asia WGS
AF:
0.144
AC:
500
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.4
DANN
Benign
0.37

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: rs11176419; hg19: chr12-67161647; API