4-117617687-A-G

Variant names:

• chr4-117617687-A-G
• rs17862054
• ENST00000422145.7:n.160-37120A>G

Variant summary

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

The ENST00000422145.7(LINC01378):​n.160-37120A>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 151,462 control chromosomes in the GnomAD database, including 2,848 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 (2848 hom., cov: 32)
• Consequence: LINC01378 ENST00000422145.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.669
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01378	NR_125757.1	n.158-37120A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01378	ENST00000422145.7	n.160-37120A>G		intron_variant	Intron 2 of 3	3
LINC01378	ENST00000600624.6	n.377-37120A>G		intron_variant	Intron 1 of 2	5
LINC01378	ENST00000615833.1	n.148+30637A>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25789 AN: 151344 Hom.: 2842 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.170 AC: 25822 AN: 151462 Hom.: 2848 Cov.: 32 AF XY: 0.167 AC XY: 12362 AN XY: 73978

African (AFR) AF: 0.310 AC: 12840 AN: 41382

American (AMR) AF: 0.119 AC: 1799 AN: 15138

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3462

East Asian (EAS) AF: 0.143 AC: 738 AN: 5154

South Asian (SAS) AF: 0.0857 AC: 413 AN: 4820

European-Finnish (FIN) AF: 0.0659 AC: 698 AN: 10586

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

European-Non Finnish (NFE) AF: 0.119 AC: 8054 AN: 67620

Other (OTH) AF: 0.190 AC: 398 AN: 2096

Alfa AF: 0.125 Hom.: 2154

Bravo AF: 0.184

Asia WGS AF: 0.125 AC: 436 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.76
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs17862054; hg19: chr4-118538842;