10-43978345-A-T

Variant names:

• chr10-43978345-A-T
• rs1254673
• ENST00000654894.1:n.557-2109A>T

Variant summary

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

The ENST00000654894.1(LINC00841):​n.557-2109A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,220 control chromosomes in the GnomAD database, including 54,471 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 0.84 (54471 hom., cov: 32)
• Consequence: LINC00841 ENST00000654894.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 4 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654894.1. 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
	LINC00841	NR_136147.1		n.398-2109A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00841	ENST00000654894.1		n.557-2109A>T		intron	N/A
	LINC00841	ENST00000660538.1		n.587-2109A>T		intron	N/A
	LINC00841	ENST00000826345.1		n.70-2109A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128271 AN: 152102 Hom.: 54438 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.906

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.903

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.837

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

GnomAD4 genome AF: 0.843 AC: 128360 AN: 152220 Hom.: 54471 Cov.: 32 AF XY: 0.841 AC XY: 62590 AN XY: 74426

African (AFR) AF: 0.750 AC: 31125 AN: 41522

American (AMR) AF: 0.794 AC: 12146 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.903 AC: 3135 AN: 3472

East Asian (EAS) AF: 0.835 AC: 4308 AN: 5158

South Asian (SAS) AF: 0.820 AC: 3952 AN: 4820

European-Finnish (FIN) AF: 0.899 AC: 9533 AN: 10604

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61303 AN: 68022

Other (OTH) AF: 0.837 AC: 1771 AN: 2116

Alfa AF: 0.878 Hom.: 6880

Bravo AF: 0.829

Asia WGS AF: 0.820 AC: 2852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.34
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs1254673; hg19: chr10-44473793;