rs6562153

chr13-61077994-T-C

Variant summary

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

The ENST00000658247.1(LINC00378):n.460+85638T>C 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 0.449 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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=-0.78).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00378	ENST00000658247.1	n.460+85638T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.537

Gnomad4 AMR AF: 0.400

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.440

Alfa AF: 0.444 Hom.: 2848

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6562153; hg19: chr13-61652128;