rs17306695

Variant names:

• chr10-85583776-G-T
• rs17306695
• ENST00000443311.3:n.164+5878G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000443311.3(GRID1-AS1):​n.164+5878G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,050 control chromosomes in the GnomAD database, including 1,194 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 0.12 (1194 hom., cov: 32)
• Consequence: GRID1-AS1 ENST00000443311.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 0 publications found

Genes affected

GRID1-AS1 (HGNC:44131): (GRID1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRID1-AS1	NR_038986.1	n.281+4173G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRID1-AS1	ENST00000443311.3	n.164+5878G>T		intron_variant	Intron 1 of 2	3
GRID1-AS1	ENST00000628016.1	n.146+5878G>T		intron_variant	Intron 1 of 1	3
GRID1-AS1	ENST00000630182.1	n.281+4173G>T		intron_variant	Intron 2 of 2	2
GRID1-AS1	ENST00000668011.2	n.261+4173G>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18054 AN: 151932 Hom.: 1191 Cov.: 32

Gnomad AFR AF: 0.0974

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.0936

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0323

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.119 AC: 18069 AN: 152050 Hom.: 1194 Cov.: 32 AF XY: 0.116 AC XY: 8658 AN XY: 74328

African (AFR) AF: 0.0974 AC: 4043 AN: 41494

American (AMR) AF: 0.0871 AC: 1329 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0936 AC: 325 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5182

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4820

European-Finnish (FIN) AF: 0.163 AC: 1723 AN: 10542

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10084 AN: 67960

Other (OTH) AF: 0.115 AC: 243 AN: 2110

Alfa AF: 0.132 Hom.: 281

Bravo AF: 0.113

Asia WGS AF: 0.0290 AC: 102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.095
DANN	Benign	0.66
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17306695; hg19: chr10-87343533;