rs10494476

Positions:

• chr1-169031256-G-A
• chr1-169031256-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.209+24928C>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 0.125 in 152,152 control chromosomes in the GnomAD database, including 1,464 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 0.13 (1464 hom., cov: 32)
• Consequence: LINC00970 NR_104091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00970	NR_104091.1	n.209+24928C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00970	ENST00000366408.3	n.209+24928C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19067 AN: 152034 Hom.: 1465 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.0881

Gnomad EAS AF: 0.0498

Gnomad SAS AF: 0.0907

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.125 AC: 19086 AN: 152152 Hom.: 1464 Cov.: 32 AF XY: 0.127 AC XY: 9465 AN XY: 74372

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.0881

Gnomad4 EAS AF: 0.0496

Gnomad4 SAS AF: 0.0912

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0870 Hom.: 1288

Bravo AF: 0.131

Asia WGS AF: 0.0750 AC: 263 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494476; hg19: chr1-169000494;