rs10748053

Variant summary

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

The NM_001366722.1(GRIP1):​c.137-9215C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 152,170 control chromosomes in the GnomAD database, including 40,659 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 0.72 ( 40659 hom., cov: 34)

Consequence

GRIP1
NM_001366722.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232
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=-0.97).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GRIP1NM_001366722.1 linkuse as main transcriptc.137-9215C>T intron_variant ENST00000359742.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GRIP1ENST00000359742.9 linkuse as main transcriptc.137-9215C>T intron_variant 5 NM_001366722.1 P1Q9Y3R0-1

Frequencies

GnomAD3 genomes
AF:
0.725
AC:
110211
AN:
152052
Hom.:
40604
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.857
Gnomad AMI
AF:
0.696
Gnomad AMR
AF:
0.715
Gnomad ASJ
AF:
0.649
Gnomad EAS
AF:
0.528
Gnomad SAS
AF:
0.629
Gnomad FIN
AF:
0.578
Gnomad MID
AF:
0.706
Gnomad NFE
AF:
0.696
Gnomad OTH
AF:
0.724
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.725
AC:
110318
AN:
152170
Hom.:
40659
Cov.:
34
AF XY:
0.718
AC XY:
53419
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.857
Gnomad4 AMR
AF:
0.716
Gnomad4 ASJ
AF:
0.649
Gnomad4 EAS
AF:
0.527
Gnomad4 SAS
AF:
0.629
Gnomad4 FIN
AF:
0.578
Gnomad4 NFE
AF:
0.696
Gnomad4 OTH
AF:
0.723
Alfa
AF:
0.697
Hom.:
48894
Bravo
AF:
0.737
Asia WGS
AF:
0.605
AC:
2106
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
CADD
Benign
7.0
DANN
Benign
0.58

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: rs10748053; hg19: chr12-66944945; API