rs10899917

Positions:

• chr10-43808168-C-G

Variant summary

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

The ENST00000659335.1(LINC00840):​n.1025+11296C>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 0.45 in 152,132 control chromosomes in the GnomAD database, including 16,177 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 0.45 (16177 hom., cov: 33)
• Consequence: LINC00840 ENST00000659335.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

Genes affected

LINC00840 (HGNC:44987): (long intergenic non-protein coding RNA 840)

LOC105378275 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378275	XR_945906.4	n.1026-10339C>G		intron_variant, non_coding_transcript_variant
LOC105378275	XR_945907.2	n.179-10339C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00840	ENST00000659335.1	n.1025+11296C>G		intron_variant, non_coding_transcript_variant
LINC00840	ENST00000666323.1	n.1010+11296C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68359 AN: 152014 Hom.: 16147 Cov.: 33

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.450 AC: 68426 AN: 152132 Hom.: 16177 Cov.: 33 AF XY: 0.447 AC XY: 33226 AN XY: 74380

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.665

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.387

Gnomad4 OTH AF: 0.438

Alfa AF: 0.417 Hom.: 1702

Bravo AF: 0.474

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.028
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10899917; hg19: chr10-44303616;