rs5754891

Positions:

• chr22-34206199-A-G
• chr22-34206199-A-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ENSG00000224404 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01643	NR_183585.1	n.912+5A>G		splice_region_variant, intron_variant
LINC01643	NR_183586.1	n.752+5A>G		splice_region_variant, intron_variant
LINC01643	NR_183587.1	n.665+5A>G		splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01643	ENST00000655904.1	n.876A>G		non_coding_transcript_exon_variant	8/8
LINC01643	ENST00000665458.1	n.1037A>G		non_coding_transcript_exon_variant	11/11
LINC01643	ENST00000665701.1	n.727A>G		non_coding_transcript_exon_variant	8/8

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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.673

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.463

Alfa AF: 0.425 Hom.: 1793

Bravo AF: 0.408

Asia WGS AF: 0.574 AC: 1996 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	1.8
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5754891; hg19: chr22-34602188;