rs9317156

Variant names:

• chr13-61054981-A-G
• rs9317156
• ENST00000658247.1:n.460+62625A>G

Variant summary

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

The ENST00000658247.1(LINC00378):​n.460+62625A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0478 in 152,196 control chromosomes in the GnomAD database, including 257 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 0.048 (257 hom., cov: 33)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

LINC00378 (HGNC:42704): (long intergenic non-protein coding RNA 378)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00378	ENST00000658247.1	n.460+62625A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0479 AC: 7281 AN: 152078 Hom.: 257 Cov.: 33

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.0649

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0478 AC: 7276 AN: 152196 Hom.: 257 Cov.: 33 AF XY: 0.0494 AC XY: 3675 AN XY: 74410

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.0420

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0648

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.0582

Gnomad4 OTH AF: 0.0531

Alfa AF: 0.0567 Hom.: 343

Bravo AF: 0.0413

Asia WGS AF: 0.0670 AC: 230 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317156; hg19: chr13-61629115;