rs77963519

Positions:

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

Variant summary

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

The XR_001751640.2(LINC01418):​n.635+24168C>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 0.0524 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 XR_001751640.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01418	XR_001751640.2	n.635+24168C>T		intron_variant, non_coding_transcript_variant
LINC01418	XR_001751639.2	n.734+13842C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01418	ENST00000559299.2	n.859+13842C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.0119

Gnomad4 AMR AF: 0.0445

Gnomad4 ASJ AF: 0.0239

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0753

Gnomad4 OTH AF: 0.0473

Alfa AF: 0.0484 Hom.: 49

Bravo AF: 0.0447

Asia WGS AF: 0.00808 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs77963519; hg19: chr15-82193846;