13-60885853-C-T

Variant names:

• chr13-60885853-C-T
• rs301640
• ENST00000658247.1:n.363+35327C>T

Variant summary

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

The ENST00000658247.1(LINC00378):​n.363+35327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 152,146 control chromosomes in the GnomAD database, including 60,451 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 0.89 (60451 hom., cov: 32)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00378	ENST00000658247.1		n.363+35327C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135437 AN: 152028 Hom.: 60415 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.909

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

GnomAD4 genome AF: 0.891 AC: 135528 AN: 152146 Hom.: 60451 Cov.: 32 AF XY: 0.892 AC XY: 66351 AN XY: 74394

African (AFR) AF: 0.861 AC: 35698 AN: 41484

American (AMR) AF: 0.929 AC: 14193 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3240 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5178 AN: 5180

South Asian (SAS) AF: 0.899 AC: 4337 AN: 4822

European-Finnish (FIN) AF: 0.902 AC: 9572 AN: 10608

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60324 AN: 67992

Other (OTH) AF: 0.911 AC: 1927 AN: 2116

Alfa AF: 0.886 Hom.: 6972

Bravo AF: 0.893

Asia WGS AF: 0.950 AC: 3301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.060
DANN	Benign	0.44
PhyloP100		-2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs301640;

hg19: chr13-61459987;