rs1414491

Variant names:

• chr10-43816910-A-G
• rs1414491
• ENST00000659335.1:n.1025+20038A>G

Variant summary

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

The ENST00000659335.1(LINC00840):​n.1025+20038A>G variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.216
• Publications: 3 publications found

Genes affected

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

LOC105378275 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659335.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00840	ENST00000659335.1		n.1025+20038A>G		intron	N/A
	LINC00840	ENST00000666323.1		n.1010+20038A>G		intron	N/A
	LINC00840	ENST00000826488.1		n.262+20038A>G		intron	N/A

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

African (AFR) AF: 0.542 AC: 22510 AN: 41504

American (AMR) AF: 0.181 AC: 2775 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.177 AC: 914 AN: 5162

South Asian (SAS) AF: 0.0823 AC: 397 AN: 4824

European-Finnish (FIN) AF: 0.121 AC: 1284 AN: 10606

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10529 AN: 68008

Other (OTH) AF: 0.232 AC: 490 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.66
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs1414491; hg19: chr10-44312358;