12-67985701-C-T

Variant names:

• chr12-67985701-C-T
• rs2906852
• ENST00000718408.1:n.391-10240C>T

Variant summary

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

The ENST00000718408.1(LINC01479):​n.391-10240C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,014 control chromosomes in the GnomAD database, including 42,354 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 0.75 (42354 hom., cov: 30)
• Consequence: LINC01479 ENST00000718408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718408.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01479	ENST00000718408.1		n.391-10240C>T		intron	N/A
	LINC01479	ENST00000718409.1		n.262-10240C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.745 AC: 113200 AN: 151896 Hom.: 42325 Cov.: 30

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.810

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.745 AC: 113282 AN: 152014 Hom.: 42354 Cov.: 30 AF XY: 0.747 AC XY: 55511 AN XY: 74296

African (AFR) AF: 0.705 AC: 29210 AN: 41434

American (AMR) AF: 0.810 AC: 12378 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2389 AN: 3472

East Asian (EAS) AF: 0.875 AC: 4528 AN: 5176

South Asian (SAS) AF: 0.788 AC: 3791 AN: 4810

European-Finnish (FIN) AF: 0.718 AC: 7572 AN: 10548

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50902 AN: 67982

Other (OTH) AF: 0.767 AC: 1619 AN: 2110

Alfa AF: 0.762 Hom.: 7537

Bravo AF: 0.752

Asia WGS AF: 0.801 AC: 2786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.59
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2906852; hg19: chr12-68379481;