rs766563

chr4-117515982-T-A

Variant summary

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

The NR_125757.1(LINC01378):n.157+87215T>A 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 0.0711 in 151,680 control chromosomes in the GnomAD database, including 637 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 0.071 (637 hom., cov: 32)
• Consequence: LINC01378 NR_125757.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

Genes affected

LINC01378 (HGNC:50645): (long intergenic non-protein coding RNA 1378)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01378	NR_125757.1	n.157+87215T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01378	ENST00000626258.2	n.201-87561T>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0709 AC: 10739 AN: 151562 Hom.: 628 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0330

Gnomad EAS AF: 0.0736

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0362

Gnomad OTH AF: 0.0635

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

GnomAD4 genome AF: 0.0711 AC: 10784 AN: 151680 Hom.: 637 Cov.: 32 AF XY: 0.0692 AC XY: 5128 AN XY: 74120

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0350

Gnomad4 ASJ AF: 0.0330

Gnomad4 EAS AF: 0.0730

Gnomad4 SAS AF: 0.0566

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0362

Gnomad4 OTH AF: 0.0637

Alfa AF: 0.0612 Hom.: 52

Bravo AF: 0.0772

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.91
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: rs766563; hg19: chr4-118437137;