rs6665379

chr1-169012926-G-Achr1-169012926-G-T

Variant summary

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

The NR_104091.1(LINC00970):n.209+43258C>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 0.136 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 NR_104091.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.779

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00970	NR_104091.1	n.209+43258C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00970	ENST00000366408.3	n.209+43258C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.0614

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00541

Gnomad4 FIN AF: 0.0220

Gnomad4 NFE AF: 0.0315

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0613 Hom.: 497

Bravo AF: 0.151

Asia WGS AF: 0.0250 AC: 87 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.44
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6665379; hg19: chr1-168982164;