rs17861942

Variant names:

• chr4-117455398-G-T
• rs17861942
• ENST00000422145.7:n.159+26631G>T

Variant summary

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

The ENST00000422145.7(LINC01378):​n.159+26631G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,006 control chromosomes in the GnomAD database, including 3,504 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 0.21 (3504 hom., cov: 33)
• Consequence: LINC01378 ENST00000422145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 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+26631G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01378	ENST00000422145.7	TSL:3	n.159+26631G>T		intron	N/A
	LINC01378	ENST00000437514.2	TSL:3	n.197-9074G>T		intron	N/A
	LINC01378	ENST00000626258.2	TSL:5	n.200+49033G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31820 AN: 151888 Hom.: 3505 Cov.: 33

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0524

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.209 AC: 31828 AN: 152006 Hom.: 3504 Cov.: 33 AF XY: 0.204 AC XY: 15155 AN XY: 74326

African (AFR) AF: 0.250 AC: 10363 AN: 41476

American (AMR) AF: 0.144 AC: 2193 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3472

East Asian (EAS) AF: 0.0525 AC: 272 AN: 5182

South Asian (SAS) AF: 0.156 AC: 754 AN: 4828

European-Finnish (FIN) AF: 0.168 AC: 1774 AN: 10572

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14856 AN: 67890

Other (OTH) AF: 0.212 AC: 448 AN: 2110

Alfa AF: 0.218 Hom.: 15664

Bravo AF: 0.210

Asia WGS AF: 0.0970 AC: 341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.36
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs17861942; hg19: chr4-118376553;