chr1-169012926-G-A

Variant names:

• chr1-169012926-G-A
• rs6665379
• ENST00000366408.3:n.209+43258C>T

Variant summary

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

The ENST00000366408.3(LINC00970):​n.209+43258C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,100 control chromosomes in the GnomAD database, including 3,586 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 0.14 (3586 hom., cov: 32)
• Consequence: LINC00970 ENST00000366408.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779
• Publications: 1 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 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.209+43258C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00970	ENST00000366408.3	TSL:1	n.209+43258C>T		intron	N/A
	LINC00970	ENST00000457405.2	TSL:3	n.472+8017C>T		intron	N/A
	LINC00970	ENST00000650631.1		n.413+8017C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20685 AN: 151982 Hom.: 3580 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0615

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00644

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0315

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.136 AC: 20721 AN: 152100 Hom.: 3586 Cov.: 32 AF XY: 0.133 AC XY: 9913 AN XY: 74380

African (AFR) AF: 0.409 AC: 16964 AN: 41434

American (AMR) AF: 0.0614 AC: 939 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.00541 AC: 26 AN: 4810

European-Finnish (FIN) AF: 0.0220 AC: 233 AN: 10600

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0315 AC: 2139 AN: 68000

Other (OTH) AF: 0.109 AC: 230 AN: 2110

Alfa AF: 0.0644 Hom.: 2211

Bravo AF: 0.151

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.44
DANN	Benign	0.82
PhyloP100		-0.78
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs6665379; hg19: chr1-168982164;