rs10489371

Positions:

• chr1-168963262-G-A
• chr1-168963262-G-C

Variant summary

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

The NR_104091.1(LINC00970):​n.210-55292C>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 0.232 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 NR_104091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00970	NR_104091.1	n.210-55292C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00970	ENST00000366408.3	n.210-55292C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.200

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.229

Alfa AF: 0.226 Hom.: 8666

Bravo AF: 0.237

Asia WGS AF: 0.421 AC: 1461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489371; hg19: chr1-168932500;