chr10-43808219-A-G

Variant names:

• chr10-43808219-A-G
• rs17463850
• ENST00000826507.1:n.1666A>G

Variant summary

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

The ENST00000826507.1(LINC00840):​n.1666A>G 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 0.0659 in 152,320 control chromosomes in the GnomAD database, including 495 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 0.066 (495 hom., cov: 33)
• Consequence: LINC00840 ENST00000826507.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 4 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826507.1. 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	ENST00000826507.1		n.1666A>G		non_coding_transcript_exon	Exon 3 of 3
	LINC00840	ENST00000659335.1		n.1025+11347A>G		intron	N/A
	LINC00840	ENST00000666323.1		n.1010+11347A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0660 AC: 10050 AN: 152202 Hom.: 494 Cov.: 33

Gnomad AFR AF: 0.0193

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.0504

Gnomad ASJ AF: 0.0997

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0523

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0671

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

GnomAD4 genome AF: 0.0659 AC: 10044 AN: 152320 Hom.: 495 Cov.: 33 AF XY: 0.0621 AC XY: 4624 AN XY: 74484

African (AFR) AF: 0.0192 AC: 799 AN: 41584

American (AMR) AF: 0.0502 AC: 769 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0997 AC: 346 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5178

South Asian (SAS) AF: 0.0602 AC: 291 AN: 4830

European-Finnish (FIN) AF: 0.0523 AC: 555 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7037 AN: 68024

Other (OTH) AF: 0.0659 AC: 139 AN: 2108

Alfa AF: 0.0813 Hom.: 74

Bravo AF: 0.0622

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.1
DANN	Benign	0.31
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs17463850; hg19: chr10-44303667;