22-34206199-A-G

Variant names:

• chr22-34206199-A-G
• rs5754891
• ENST00000655904.1:n.876A>G

Variant summary

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

The NR_183585.1(LINC01643):​n.912+5A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,890 control chromosomes in the GnomAD database, including 14,268 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 0.42 (14268 hom., cov: 31)
• Consequence: LINC01643 NR_183585.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 8 publications found

Genes affected

LINC01643 (HGNC:52430): (long intergenic non-protein coding RNA 1643)

ENSG00000224404 (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 (SAS) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183585.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01643	NR_183585.1		n.912+5A>G		splice_region intron	N/A
	LINC01643	NR_183586.1		n.752+5A>G		splice_region intron	N/A
	LINC01643	NR_183587.1		n.665+5A>G		splice_region intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01643	ENST00000655904.1		n.876A>G		non_coding_transcript_exon	Exon 8 of 8
	LINC01643	ENST00000665458.1		n.1037A>G		non_coding_transcript_exon	Exon 11 of 11
	LINC01643	ENST00000665701.1		n.727A>G		non_coding_transcript_exon	Exon 8 of 8

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63851 AN: 151772 Hom.: 14257 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.421 AC: 63889 AN: 151890 Hom.: 14268 Cov.: 31 AF XY: 0.425 AC XY: 31567 AN XY: 74198

African (AFR) AF: 0.294 AC: 12172 AN: 41436

American (AMR) AF: 0.385 AC: 5888 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3468

East Asian (EAS) AF: 0.610 AC: 3127 AN: 5124

South Asian (SAS) AF: 0.673 AC: 3229 AN: 4798

European-Finnish (FIN) AF: 0.440 AC: 4642 AN: 10556

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.462 AC: 31389 AN: 67920

Other (OTH) AF: 0.463 AC: 976 AN: 2108

Alfa AF: 0.419 Hom.: 1825

Bravo AF: 0.408

Asia WGS AF: 0.574 AC: 1996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.8
DANN	Benign	0.26
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs5754891; hg19: chr22-34602188;