rs6562160

Positions:

• chr13-61127372-C-A
• chr13-61127372-C-G

Variant summary

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

The ENST00000658247.1(LINC00378):​n.461-49157C>A 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 0.4 in 150,886 control chromosomes in the GnomAD database, including 12,258 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 0.40 (12258 hom., cov: 28)
• Consequence: LINC00378 ENST00000658247.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.436 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.461-49157C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60332 AN: 150768 Hom.: 12242 Cov.: 28

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.400 AC: 60381 AN: 150886 Hom.: 12258 Cov.: 28 AF XY: 0.398 AC XY: 29330 AN XY: 73692

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.397

Alfa AF: 0.419 Hom.: 1689

Bravo AF: 0.397

Asia WGS AF: 0.308 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.79
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6562160; hg19: chr13-61701506;