1-168963262-G-A

Variant names:

• chr1-168963262-G-A
• rs10489371
• ENST00000366408.3:n.210-55292C>T

Variant summary

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

The ENST00000366408.3(LINC00970):​n.210-55292C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,104 control chromosomes in the GnomAD database, including 4,514 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 0.23 (4514 hom., cov: 32)
• Consequence: LINC00970 ENST00000366408.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47
• Publications: 6 publications found

Genes affected

LINC00970 (HGNC:):

LINC00970 (HGNC:48730): (long intergenic non-protein coding RNA 970)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000366408.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00970	NR_104091.1		n.210-55292C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00970	ENST00000366408.3	TSL:1	n.210-55292C>T		intron	N/A
	LINC00970	ENST00000457405.2	TSL:3	n.472+57681C>T		intron	N/A
	LINC00970	ENST00000650631.1		n.413+57681C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35221 AN: 151986 Hom.: 4502 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.232 AC: 35264 AN: 152104 Hom.: 4514 Cov.: 32 AF XY: 0.235 AC XY: 17445 AN XY: 74334

African (AFR) AF: 0.200 AC: 8294 AN: 41498

American (AMR) AF: 0.267 AC: 4078 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 821 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3024 AN: 5160

South Asian (SAS) AF: 0.326 AC: 1569 AN: 4814

European-Finnish (FIN) AF: 0.217 AC: 2294 AN: 10574

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14581 AN: 67976

Other (OTH) AF: 0.229 AC: 485 AN: 2114

Alfa AF: 0.227 Hom.: 14278

Bravo AF: 0.237

Asia WGS AF: 0.421 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.72
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10489371; hg19: chr1-168932500;