rs2387742

Positions:

• chr10-6794725-C-T

Variant summary

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

The ENST00000436383.2(LINC00707):​n.501+13239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 152,048 control chromosomes in the GnomAD database, including 567 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 0.064 (567 hom., cov: 31)
• Consequence: LINC00707 ENST00000436383.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

Genes affected

LINC00707 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00707	NR_038291.1	n.473+13239C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00707	ENST00000436383.2	n.501+13239C>T		intron_variant		2
LINC00707	ENST00000648093.1	n.522+13239C>T		intron_variant
LINC00707	ENST00000648398.1	n.483+13239C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0636 AC: 9662 AN: 151930 Hom.: 568 Cov.: 31

Gnomad AFR AF: 0.0166

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0813

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0154

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0726

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0635 AC: 9657 AN: 152048 Hom.: 567 Cov.: 31 AF XY: 0.0635 AC XY: 4717 AN XY: 74340

Gnomad4 AFR AF: 0.0165

Gnomad4 AMR AF: 0.0813

Gnomad4 ASJ AF: 0.0395

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.0154

Gnomad4 NFE AF: 0.0726

Gnomad4 OTH AF: 0.0726

Alfa AF: 0.0733 Hom.: 220

Bravo AF: 0.0657

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2387742; hg19: chr10-6836687;