rs10507662

Variant names:

• chr13-61084730-T-C
• rs10507662
• ENST00000658247.1:n.461-91799T>C

Variant summary

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

The ENST00000658247.1(LINC00378):​n.461-91799T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0476 in 152,212 control chromosomes in the GnomAD database, including 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 0.048 (258 hom., cov: 32)
• Consequence: LINC00378 ENST00000658247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0938 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.461-91799T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0477 AC: 7255 AN: 152094 Hom.: 258 Cov.: 32

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0419

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0644

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0476 AC: 7250 AN: 152212 Hom.: 258 Cov.: 32 AF XY: 0.0492 AC XY: 3661 AN XY: 74400

Gnomad4 AFR AF: 0.0105

Gnomad4 AMR AF: 0.0418

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0643

Gnomad4 FIN AF: 0.0873

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0547 Hom.: 118

Bravo AF: 0.0412

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507662; hg19: chr13-61658864;