ENST00000458168.2:n.512C>T

Variant names:

• chr10-9286688-C-T
• rs10491003
• ENST00000458168.2:n.512C>T

Variant summary

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

The ENST00000458168.2(LINC00709):​n.512C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,186 control chromosomes in the GnomAD database, including 1,045 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 0.11 (1045 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: LINC00709 ENST00000458168.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 26 publications found

Genes affected

LINC00709 (HGNC:44700): (long intergenic non-protein coding RNA 709)

LOC101928272 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00709	NR_108039.1	n.345C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LOC101928272	NR_120635.1	n.193-2299G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00709	ENST00000458168.2	n.512C>T		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16734 AN: 152064 Hom.: 1041 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.0223

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0927

Gnomad OTH AF: 0.102

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AC: 0 AN: 0

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.110 AC: 16774 AN: 152182 Hom.: 1045 Cov.: 32 AF XY: 0.113 AC XY: 8445 AN XY: 74412

African (AFR) AF: 0.122 AC: 5058 AN: 41506

American (AMR) AF: 0.204 AC: 3120 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0965 AC: 335 AN: 3470

East Asian (EAS) AF: 0.0224 AC: 116 AN: 5184

South Asian (SAS) AF: 0.0689 AC: 333 AN: 4830

European-Finnish (FIN) AF: 0.111 AC: 1171 AN: 10578

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0927 AC: 6302 AN: 68008

Other (OTH) AF: 0.101 AC: 212 AN: 2108

Alfa AF: 0.0946 Hom.: 1650

Bravo AF: 0.117

Asia WGS AF: 0.0630 AC: 218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs10491003; hg19: chr10-9328651;