rs7980416

Variant names:

• chr12-67947042-C-T
• rs7980416
• ENST00000546170.1:n.238+14653C>T

Variant summary

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

The ENST00000546170.1(LINC01479):​n.238+14653C>T variant causes a intron 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 ENST00000546170.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 5 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546170.1. 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
	LINC01479	NR_120456.1		n.266+14653C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01479	ENST00000546170.1	TSL:2	n.238+14653C>T		intron	N/A
	LINC01479	ENST00000718408.1		n.390+17655C>T		intron	N/A
	LINC01479	ENST00000718409.1		n.261+14675C>T		intron	N/A

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

African (AFR) AF: 0.410 AC: 16979 AN: 41414

American (AMR) AF: 0.363 AC: 5537 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3470

East Asian (EAS) AF: 0.468 AC: 2411 AN: 5152

South Asian (SAS) AF: 0.325 AC: 1562 AN: 4810

European-Finnish (FIN) AF: 0.216 AC: 2276 AN: 10542

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12421 AN: 67986

Other (OTH) AF: 0.267 AC: 564 AN: 2110

Alfa AF: 0.221 Hom.: 13458

Bravo AF: 0.300

Asia WGS AF: 0.372 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.77
DANN	Benign	0.29
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7980416; hg19: chr12-68340822;