rs1489550

Variant names:

• chr4-117604999-A-G
• rs1489550
• ENST00000422145.7:n.160-49808A>G

Variant summary

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

The ENST00000422145.7(LINC01378):​n.160-49808A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,936 control chromosomes in the GnomAD database, including 2,866 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 0.17 (2866 hom., cov: 32)
• Consequence: LINC01378 ENST00000422145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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.158-49808A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01378	ENST00000422145.7	TSL:3	n.160-49808A>G		intron	N/A
	LINC01378	ENST00000600624.6	TSL:5	n.376+32864A>G		intron	N/A
	LINC01378	ENST00000615833.1	TSL:5	n.148+17949A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25869 AN: 151820 Hom.: 2860 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.170 AC: 25902 AN: 151936 Hom.: 2866 Cov.: 32 AF XY: 0.167 AC XY: 12389 AN XY: 74250

African (AFR) AF: 0.310 AC: 12861 AN: 41436

American (AMR) AF: 0.120 AC: 1824 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3468

East Asian (EAS) AF: 0.144 AC: 743 AN: 5152

South Asian (SAS) AF: 0.0856 AC: 412 AN: 4812

European-Finnish (FIN) AF: 0.0655 AC: 694 AN: 10590

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8082 AN: 67904

Other (OTH) AF: 0.191 AC: 402 AN: 2106

Alfa AF: 0.129 Hom.: 1002

Bravo AF: 0.184

Asia WGS AF: 0.125 AC: 435 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.53
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs1489550; hg19: chr4-118526154;