rs10507662

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.89).
• 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

African (AFR) AF: 0.0105 AC: 438 AN: 41568

American (AMR) AF: 0.0418 AC: 639 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3468

East Asian (EAS) AF: 0.101 AC: 520 AN: 5150

South Asian (SAS) AF: 0.0643 AC: 310 AN: 4824

European-Finnish (FIN) AF: 0.0873 AC: 926 AN: 10606

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0579 AC: 3935 AN: 68008

Other (OTH) AF: 0.0535 AC: 113 AN: 2112

Alfa AF: 0.0546 Hom.: 128

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10507662; hg19: chr13-61658864;