rs2749135

Positions:

• chr6-101043549-G-A
• chr6-101043549-G-C

Variant summary

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

The ENST00000683774.1(GRIK2):​n.51+80798G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,120 control chromosomes in the GnomAD database, including 35,840 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 0.68 (35840 hom., cov: 32)
• Consequence: GRIK2 ENST00000683774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370

Genes affected

GRIK2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984041	XR_002956381.2	n.312+80798G>A		intron_variant
LOC107984041	XR_007059692.1	n.312+80798G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRIK2	ENST00000683774.1	n.51+80798G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103980 AN: 152002 Hom.: 35811 Cov.: 32

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.684 AC: 104063 AN: 152120 Hom.: 35840 Cov.: 32 AF XY: 0.679 AC XY: 50448 AN XY: 74346

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.690

Alfa AF: 0.686 Hom.: 14429

Bravo AF: 0.689

Asia WGS AF: 0.594 AC: 2063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2749135; hg19: chr6-101491425;