rs898549

Positions:

• chr10-43963266-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_136147.1(LINC00841):​n.397+7951C>T variant causes a intron, non coding transcript 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 NR_136147.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.858

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00841	NR_136147.1	n.397+7951C>T		intron_variant, non_coding_transcript_variant
LINC00841	NR_033846.2	n.613-2117C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00841	ENST00000660538.1	n.417-3279C>T		intron_variant, non_coding_transcript_variant
LINC00841	ENST00000654894.1	n.277-2117C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.474

Alfa AF: 0.554 Hom.: 24517

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs898549; hg19: chr10-44458714;