chr10-85934535-T-C

Position:

• chr10-85934535-T-C

Variant summary

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

The NM_017551.3(GRID1):​c.727-18296A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 151,994 control chromosomes in the GnomAD database, including 872 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 0.097 (872 hom., cov: 31)
• Consequence: GRID1 NM_017551.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

GRID1 (HGNC:4575): (glutamate ionotropic receptor delta type subunit 1) This gene encodes a subunit of glutamate receptor channels. These channels mediate most of the fast excitatory synaptic transmission in the central nervous system and play key roles in synaptic plasticity.[provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GRID1	NM_017551.3	c.727-18296A>G		intron_variant		ENST00000327946.12	NP_060021.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRID1	ENST00000327946.12	c.727-18296A>G		intron_variant		2	NM_017551.3	ENSP00000330148.7
GRID1	ENST00000464741.2	n.727-18296A>G		intron_variant		1		ENSP00000433064.1

Frequencies

GnomAD3 genomes AF: 0.0974 AC: 14786 AN: 151876 Hom.: 872 Cov.: 31

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.00638

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.0973 AC: 14785 AN: 151994 Hom.: 872 Cov.: 31 AF XY: 0.0959 AC XY: 7126 AN XY: 74290

Gnomad4 AFR AF: 0.0434

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.00601

Gnomad4 SAS AF: 0.0910

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.134

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0838 Hom.: 190

Bravo AF: 0.0948

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.093
DANN	Benign	0.70

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: rs76765968; hg19: chr10-87694292;