rs766563

Variant names:

• chr4-117515982-T-A
• rs766563
• ENST00000422145.7:n.159+87215T>A

Variant summary

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

The ENST00000422145.7(LINC01378):​n.159+87215T>A variant causes a intron 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 ENST00000422145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422145.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01378	NR_125757.1		n.157+87215T>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01378	ENST00000422145.7	TSL:3	n.159+87215T>A		intron	N/A
	LINC01378	ENST00000437514.2	TSL:3	n.348-24115T>A		intron	N/A
	LINC01378	ENST00000626258.2	TSL:5	n.201-87561T>A		intron	N/A

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

African (AFR) AF: 0.163 AC: 6768 AN: 41410

American (AMR) AF: 0.0350 AC: 531 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.0330 AC: 114 AN: 3454

East Asian (EAS) AF: 0.0730 AC: 376 AN: 5152

South Asian (SAS) AF: 0.0566 AC: 273 AN: 4822

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10598

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0362 AC: 2454 AN: 67770

Other (OTH) AF: 0.0637 AC: 134 AN: 2102

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.48
PhyloP100		-0.51

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs766563;

hg19: chr4-118437137;