rs7980416

chr12-67947042-C-T

Variant summary

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

The NR_120456.1(LINC01479):n.266+14653C>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 0.281 in 151,958 control chromosomes in the GnomAD database, including 6,991 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 0.28 (6991 hom., cov: 31)
• Consequence: LINC01479 NR_120456.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

LINC01479 (HGNC:51123): (long intergenic non-protein coding RNA 1479)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01479	NR_120456.1	n.266+14653C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01479	ENST00000546170.1	n.238+14653C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42592 AN: 151840 Hom.: 6970 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.281 AC: 42652 AN: 151958 Hom.: 6991 Cov.: 31 AF XY: 0.285 AC XY: 21173 AN XY: 74268

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.194

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.267

Alfa AF: 0.206 Hom.: 7508

Bravo AF: 0.300

Asia WGS AF: 0.372 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.77
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7980416; hg19: chr12-68340822;