ENST00000826507.1:n.2221C>A

Variant names:

• chr10-43808774-C-A
• rs1537796
• ENST00000826507.1:n.2221C>A

Variant summary

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

The ENST00000826507.1(LINC00840):​n.2221C>A 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 0.428 in 151,958 control chromosomes in the GnomAD database, including 14,357 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 0.43 (14357 hom., cov: 32)
• Consequence: LINC00840 ENST00000826507.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• 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=-0.95).
• 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 rank	MANE	Protein	UniProt
LOC105378275	XR_945906.4	n.1026-9733C>A		intron_variant	Intron 2 of 2
LOC105378275	XR_945907.2	n.179-9733C>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00840	ENST00000826507.1	n.2221C>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00840	ENST00000659335.1	n.1025+11902C>A		intron_variant	Intron 2 of 4
LINC00840	ENST00000666323.1	n.1010+11902C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64907 AN: 151838 Hom.: 14328 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.428 AC: 64970 AN: 151958 Hom.: 14357 Cov.: 32 AF XY: 0.425 AC XY: 31593 AN XY: 74288

African (AFR) AF: 0.499 AC: 20649 AN: 41416

American (AMR) AF: 0.450 AC: 6883 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1356 AN: 3472

East Asian (EAS) AF: 0.665 AC: 3438 AN: 5172

South Asian (SAS) AF: 0.287 AC: 1386 AN: 4822

European-Finnish (FIN) AF: 0.334 AC: 3520 AN: 10538

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26249 AN: 67946

Other (OTH) AF: 0.423 AC: 890 AN: 2102

Alfa AF: 0.369 Hom.: 5452

Bravo AF: 0.449

Asia WGS AF: 0.466 AC: 1623 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	3.1
DANN	Benign	0.27
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs1537796; hg19: chr10-44304222;