rs10495113

Positions:

• chr1-218915586-T-C

Variant summary

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

The NR_146917.1(LINC01710):​n.98-268A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 152,342 control chromosomes in the GnomAD database, including 295 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 0.024 (295 hom., cov: 33)
• Consequence: LINC01710 NR_146917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

Genes affected

LINC01710 (HGNC:52498): (long intergenic non-protein coding RNA 1710)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01710	NR_146917.1	n.98-268A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01710	ENST00000655362.1	n.491-268A>G		intron_variant, non_coding_transcript_variant
LINC01710	ENST00000446002.1	n.48-268A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0237 AC: 3615 AN: 152224 Hom.: 292 Cov.: 33

Gnomad AFR AF: 0.00779

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00688

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0238 AC: 3633 AN: 152342 Hom.: 295 Cov.: 33 AF XY: 0.0272 AC XY: 2030 AN XY: 74498

Gnomad4 AFR AF: 0.00781

Gnomad4 AMR AF: 0.0350

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.00358

Gnomad4 NFE AF: 0.00689

Gnomad4 OTH AF: 0.0397

Alfa AF: 0.0162 Hom.: 30

Bravo AF: 0.0259

Asia WGS AF: 0.205 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495113; hg19: chr1-219088928;