rs1414491

Positions:

• chr10-43816910-A-G

Variant summary

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

The ENST00000659335.1(LINC00840):​n.1025+20038A>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 0.26 in 152,182 control chromosomes in the GnomAD database, including 7,483 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 0.26 (7483 hom., cov: 33)
• Consequence: LINC00840 ENST00000659335.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216

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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378275	XR_945906.4	n.1026-1597A>G		intron_variant, non_coding_transcript_variant
LOC105378275	XR_945907.2	n.179-1597A>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+20038A>G		intron_variant, non_coding_transcript_variant
LINC00840	ENST00000666323.1	n.1010+20038A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39435 AN: 152064 Hom.: 7452 Cov.: 33

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.260 AC: 39513 AN: 152182 Hom.: 7483 Cov.: 33 AF XY: 0.253 AC XY: 18785 AN XY: 74390

Gnomad4 AFR AF: 0.542

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.0823

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.232

Alfa AF: 0.205 Hom.: 785

Bravo AF: 0.281

Asia WGS AF: 0.156 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1414491; hg19: chr10-44312358;