1-169080643-G-A

Variant names:

• chr1-169080643-G-A
• rs1200100
• ENST00000366408.3:n.51+6312C>T

Variant summary

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

The ENST00000366408.3(LINC00970):​n.51+6312C>T variant causes a intron 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 ENST00000366408.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 5 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=-0.89).
• 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 rank	MANE	Protein	UniProt
LINC00970	NR_104091.1	n.51+6312C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00970	ENST00000366408.3	n.51+6312C>T		intron_variant	Intron 1 of 4	1
LINC00970	ENST00000457405.2	n.53+6312C>T		intron_variant	Intron 1 of 7	3
LINC00970	ENST00000650631.1	n.132-20124C>T		intron_variant	Intron 1 of 8

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

African (AFR) AF: 0.269 AC: 10793 AN: 40168

American (AMR) AF: 0.456 AC: 6775 AN: 14866

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 1994 AN: 3450

East Asian (EAS) AF: 0.272 AC: 1354 AN: 4986

South Asian (SAS) AF: 0.441 AC: 2049 AN: 4646

European-Finnish (FIN) AF: 0.650 AC: 6336 AN: 9748

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.635 AC: 42939 AN: 67622

Other (OTH) AF: 0.531 AC: 1102 AN: 2074

Alfa AF: 0.598 Hom.: 44353

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
PhyloP100		-0.094

Splicing

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

Other links and lift over

dbSNP: rs1200100; hg19: chr1-169049881;