rs4778944

Positions:

• chr15-81911334-T-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+14339A>G 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 0.417 in 152,038 control chromosomes in the GnomAD database, including 13,518 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 0.42 (13518 hom., cov: 32)
• Consequence: LINC01418 XR_001751640.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01418	XR_001751640.2	n.635+14339A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01418	ENST00000559299.2	n.859+4013A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63373 AN: 151920 Hom.: 13499 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.417 AC: 63431 AN: 152038 Hom.: 13518 Cov.: 32 AF XY: 0.422 AC XY: 31343 AN XY: 74330

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.420

Alfa AF: 0.417 Hom.: 17772

Bravo AF: 0.403

Asia WGS AF: 0.399 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	8.3
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4778944; hg19: chr15-82203675;