rs11562935

chr4-117554174-G-A

Variant summary

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

The NR_125757.1(LINC01378):n.158-100633G>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 0.0322 in 151,684 control chromosomes in the GnomAD database, including 110 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 0.032 (110 hom., cov: 31)
• Consequence: LINC01378 NR_125757.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01378	NR_125757.1	n.158-100633G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01378	ENST00000626258.2	n.201-49369G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0321 AC: 4869 AN: 151564 Hom.: 109 Cov.: 31

Gnomad AFR AF: 0.0618

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0180

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.0739

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.00646

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.0393

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

GnomAD4 genome AF: 0.0322 AC: 4881 AN: 151684 Hom.: 110 Cov.: 31 AF XY: 0.0320 AC XY: 2374 AN XY: 74146

Gnomad4 AFR AF: 0.0619

Gnomad4 AMR AF: 0.0179

Gnomad4 ASJ AF: 0.0188

Gnomad4 EAS AF: 0.0733

Gnomad4 SAS AF: 0.0496

Gnomad4 FIN AF: 0.00646

Gnomad4 NFE AF: 0.0178

Gnomad4 OTH AF: 0.0399

Alfa AF: 0.0326 Hom.: 19

Bravo AF: 0.0345

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.8
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11562935; hg19: chr4-118475329;