rs1200100

Positions:

• chr1-169080643-G-A
• chr1-169080643-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.51+6312C>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 0.498 in 148,762 control chromosomes in the GnomAD database, including 20,436 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 0.50 (20436 hom., cov: 27)
• Consequence: LINC00970 NR_104091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00970	NR_104091.1	n.51+6312C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00970	ENST00000366408.3	n.51+6312C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.498 AC: 74095 AN: 148662 Hom.: 20433 Cov.: 27

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.498 AC: 74115 AN: 148762 Hom.: 20436 Cov.: 27 AF XY: 0.496 AC XY: 35875 AN XY: 72376

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.531

Alfa AF: 0.601 Hom.: 37570

Bravo AF: 0.469

Asia WGS AF: 0.321 AC: 1112 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1200100; hg19: chr1-169049881;