10-85583776-G-T

Position:

• chr10-85583776-G-T

Variant summary

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

The NR_038986.1(GRID1-AS1):​n.281+4173G>T 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 0.119 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 NR_038986.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
GRID1-AS1	NR_038986.1	n.281+4173G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GRID1-AS1	ENST00000630182.1	n.281+4173G>T		intron_variant, non_coding_transcript_variant		2
GRID1-AS1	ENST00000443311.2	n.40+5878G>T		intron_variant, non_coding_transcript_variant		3
GRID1-AS1	ENST00000628016.1	n.146+5878G>T		intron_variant, non_coding_transcript_variant		3
GRID1-AS1	ENST00000668011.1	n.253+4173G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0974

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.0936

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.115

Alfa AF: 0.134 Hom.: 276

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17306695; hg19: chr10-87343533;