13-61054981-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658247.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00378	ENST00000658247.1		n.460+62625A>G		intron	N/A

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

African (AFR) AF: 0.0104 AC: 432 AN: 41568

American (AMR) AF: 0.0420 AC: 642 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3470

East Asian (EAS) AF: 0.101 AC: 525 AN: 5174

South Asian (SAS) AF: 0.0648 AC: 312 AN: 4816

European-Finnish (FIN) AF: 0.0876 AC: 927 AN: 10582

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0582 AC: 3956 AN: 67982

Other (OTH) AF: 0.0531 AC: 112 AN: 2110

Alfa AF: 0.0548 Hom.: 418

Bravo AF: 0.0413

Asia WGS AF: 0.0670 AC: 230 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.50
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs9317156; hg19: chr13-61629115;