rs11176482

chr12-66902767-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007063353.1(LOC124902956):n.20178A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,134 control chromosomes in the GnomAD database, including 5,550 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 (5550 hom., cov: 33)
• Consequence: LOC124902956 XR_007063353.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643

Genes affected

LOC124902956 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902956	XR_007063353.1	n.20178A>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIP1	ENST00000643019.1	c.58+166283A>G		intron_variant
GRIP1	ENST00000535721.1	n.114-10813A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39489 AN: 152016 Hom.: 5533 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.237

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.260 AC: 39518 AN: 152134 Hom.: 5550 Cov.: 33 AF XY: 0.268 AC XY: 19947 AN XY: 74364

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.235

Alfa AF: 0.261 Hom.: 1291

Bravo AF: 0.242

Asia WGS AF: 0.354 AC: 1227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.7
Dann	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11176482; hg19: chr12-67296547;