ENST00000659335.1:n.1025+15680G>A

Variant names:

• chr10-43812552-G-A
• rs7900896
• ENST00000659335.1:n.1025+15680G>A

Variant summary

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

The ENST00000659335.1(LINC00840):​n.1025+15680G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,910 control chromosomes in the GnomAD database, including 10,240 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 0.36 (10240 hom., cov: 31)
• Consequence: LINC00840 ENST00000659335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378275	XR_945906.4	n.1026-5955G>A		intron_variant	Intron 2 of 2
LOC105378275	XR_945907.2	n.179-5955G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00840	ENST00000659335.1	n.1025+15680G>A		intron_variant	Intron 2 of 4
LINC00840	ENST00000666323.1	n.1010+15680G>A		intron_variant	Intron 2 of 3
LINC00840	ENST00000826488.1	n.262+15680G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53947 AN: 151792 Hom.: 10205 Cov.: 31

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.356 AC: 54023 AN: 151910 Hom.: 10240 Cov.: 31 AF XY: 0.348 AC XY: 25855 AN XY: 74236

African (AFR) AF: 0.481 AC: 19926 AN: 41388

American (AMR) AF: 0.288 AC: 4402 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1090 AN: 3466

East Asian (EAS) AF: 0.355 AC: 1827 AN: 5144

South Asian (SAS) AF: 0.224 AC: 1075 AN: 4804

European-Finnish (FIN) AF: 0.232 AC: 2446 AN: 10558

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22039 AN: 67958

Other (OTH) AF: 0.342 AC: 723 AN: 2114

Alfa AF: 0.336 Hom.: 20979

Bravo AF: 0.371

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.6
DANN	Benign	0.62
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs7900896; hg19: chr10-44308000;