rs77963519

Variant names:

• chr15-81901505-G-A
• rs77963519
• ENST00000559299.2:n.859+13842C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-81901505-G-A
• chr15-81901505-G-C

Variant summary

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

The ENST00000559299.2(LINC01418):​n.859+13842C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0524 in 152,250 control chromosomes in the GnomAD database, including 300 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 0.052 (300 hom., cov: 33)
• Consequence: LINC01418 ENST00000559299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 3 publications found

Genes affected

LINC01418 (HGNC:50711): (long intergenic non-protein coding RNA 1418)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559299.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01418	ENST00000559299.2	TSL:4	n.859+13842C>T		intron	N/A
	LINC01418	ENST00000829414.1		n.978+24168C>T		intron	N/A
	LINC01418	ENST00000829415.1		n.428+24168C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0524 AC: 7979 AN: 152132 Hom.: 300 Cov.: 33

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.0446

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0157

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0753

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0524 AC: 7974 AN: 152250 Hom.: 300 Cov.: 33 AF XY: 0.0530 AC XY: 3943 AN XY: 74436

African (AFR) AF: 0.0119 AC: 493 AN: 41564

American (AMR) AF: 0.0445 AC: 681 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5174

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1279 AN: 10600

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0753 AC: 5120 AN: 68006

Other (OTH) AF: 0.0473 AC: 100 AN: 2114

Alfa AF: 0.0474 Hom.: 49

Bravo AF: 0.0447

Asia WGS AF: 0.00808 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.39
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs77963519; hg19: chr15-82193846;