12-66347757-AT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001366722.1(GRIP1):c.*1261del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.46 (16051 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: GRIP1 NM_001366722.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.240

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 12-66347757-AT-A is Benign according to our data. Variant chr12-66347757-AT-A is described in ClinVar as [Benign]. Clinvar id is 310277.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRIP1	NM_001366722.1	c.*1261del		3_prime_UTR_variant	25/25	ENST00000359742.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIP1	ENST00000359742.9	c.*1261del		3_prime_UTR_variant	25/25	5	NM_001366722.1	P1
GRIP1	ENST00000398016.7	c.*1261del		3_prime_UTR_variant	24/24	1
GRIP1	ENST00000696989.1	c.*1261del		3_prime_UTR_variant	23/23

Frequencies

GnomAD3 genomes AF: 0.456 AC: 68843 AN: 151126 Hom.: 16041 Cov.: 0

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.434

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.456 AC: 68893 AN: 151246 Hom.: 16051 Cov.: 0 AF XY: 0.463 AC XY: 34211 AN XY: 73858

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.435

Bravo AF: 0.466

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Fraser syndrome 1 Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs35499444; hg19: chr12-66741537;