rs6562153

Variant names:

• chr13-61077994-T-C
• rs6562153
• ENST00000658247.1:n.460+85638T>C

Variant summary

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

The ENST00000658247.1(LINC00378):​n.460+85638T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,938 control chromosomes in the GnomAD database, including 15,630 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 0.45 (15630 hom., cov: 32)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 3 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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 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+85638T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68082 AN: 151820 Hom.: 15596 Cov.: 32

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.449 AC: 68179 AN: 151938 Hom.: 15630 Cov.: 32 AF XY: 0.445 AC XY: 33043 AN XY: 74256

African (AFR) AF: 0.537 AC: 22224 AN: 41420

American (AMR) AF: 0.400 AC: 6110 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3472

East Asian (EAS) AF: 0.339 AC: 1748 AN: 5162

South Asian (SAS) AF: 0.403 AC: 1942 AN: 4822

European-Finnish (FIN) AF: 0.401 AC: 4236 AN: 10568

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28957 AN: 67930

Other (OTH) AF: 0.440 AC: 924 AN: 2102

Alfa AF: 0.446 Hom.: 2957

Bravo AF: 0.453

Asia WGS AF: 0.378 AC: 1317 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	14
DANN	Benign	0.60
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6562153; hg19: chr13-61652128;