rs6562160

Variant names:

• chr13-61127372-C-A
• rs6562160
• ENST00000658247.1:n.461-49157C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000658247.1(LINC00378):​n.461-49157C>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372
• Publications: 0 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=-0.95).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00378	ENST00000658247.1	n.461-49157C>A		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.352 AC: 14440 AN: 41040

American (AMR) AF: 0.374 AC: 5666 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1368 AN: 3456

East Asian (EAS) AF: 0.333 AC: 1704 AN: 5110

South Asian (SAS) AF: 0.338 AC: 1610 AN: 4768

European-Finnish (FIN) AF: 0.429 AC: 4458 AN: 10384

Middle Eastern (MID) AF: 0.434 AC: 126 AN: 290

European-Non Finnish (NFE) AF: 0.441 AC: 29817 AN: 67678

Other (OTH) AF: 0.397 AC: 829 AN: 2090

Alfa AF: 0.416 Hom.: 1735

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
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6562160; hg19: chr13-61701506;