rs898549

Variant names:

• chr10-43963266-C-T
• rs898549
• ENST00000654894.1:n.277-2117C>T

Variant summary

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

The ENST00000654894.1(LINC00841):​n.277-2117C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,058 control chromosomes in the GnomAD database, including 18,041 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 0.44 (18041 hom., cov: 32)
• Consequence: LINC00841 ENST00000654894.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.858
• Publications: 13 publications found

Genes affected

LINC00841 (HGNC:27430): (long intergenic non-protein coding RNA 841)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00841	NR_033846.2	n.613-2117C>T		intron_variant	Intron 5 of 7
LINC00841	NR_136147.1	n.397+7951C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00841	ENST00000654894.1	n.277-2117C>T		intron_variant	Intron 3 of 5
LINC00841	ENST00000660538.1	n.417-3279C>T		intron_variant	Intron 4 of 5
LINC00841	ENST00000826345.1	n.70-17188C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67395 AN: 151940 Hom.: 18037 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.443 AC: 67400 AN: 152058 Hom.: 18041 Cov.: 32 AF XY: 0.441 AC XY: 32765 AN XY: 74322

African (AFR) AF: 0.143 AC: 5940 AN: 41476

American (AMR) AF: 0.404 AC: 6175 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2030 AN: 3470

East Asian (EAS) AF: 0.390 AC: 2011 AN: 5162

South Asian (SAS) AF: 0.453 AC: 2183 AN: 4820

European-Finnish (FIN) AF: 0.571 AC: 6034 AN: 10570

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41346 AN: 67966

Other (OTH) AF: 0.474 AC: 1003 AN: 2114

Alfa AF: 0.512 Hom.: 33965

Bravo AF: 0.414

Asia WGS AF: 0.417 AC: 1454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	13
DANN	Benign	0.62
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs898549; hg19: chr10-44458714;