Variant chr12-66971260-C-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000652412.1(ENSG00000257083):n.516-7095G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,978 control chromosomes in the GnomAD database, including 4,183 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 0.22 ( 4183 hom., cov: 32)

Consequence

ENST00000652412.1 intron, non_coding_transcript

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Variant links:

Genes affected

(HGNC:):

links:

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]

GRIP1 links:

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=-0.97).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
GRIP1	NM_001379349.1 linkuse as main transcript	c.58+97790G>A	intron_variant
GRIP1	NM_001379351.1 linkuse as main transcript	c.58+97790G>A	intron_variant
GRIP1	XM_005268754.5 linkuse as main transcript	c.58+97790G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
	ENST00000652412.1 linkuse as main transcript	n.516-7095G>A	intron_variant, non_coding_transcript_variant
GRIP1	ENST00000643019.1 linkuse as main transcript	c.58+97790G>A	intron_variant
GRIP1	ENST00000535721.1 linkuse as main transcript	n.114-79306G>A	intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.223

AC:

33835

AN:

151860

Hom.:

4175

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.276

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.215

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.352

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.255

Gnomad OTH

AF:

0.195

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

GnomAD4 genome

AF:

0.223

AC:

33869

AN:

151978

Hom.:

4183

Cov.:

AF XY:

0.231

AC XY:

17129

AN XY:

74266

show subpopulations

Gnomad4 AFR

AF:

0.127

Gnomad4 AMR

AF:

0.241

Gnomad4 ASJ

AF:

0.215

Gnomad4 EAS

AF:

0.249

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.352

Gnomad4 NFE

AF:

0.255

Gnomad4 OTH

AF:

0.194

Alfa

AF:

0.153

Hom.:

342

Bravo

AF:

0.209

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.038

DANN

Benign

0.27

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over