22-34137753-C-T

Variant names:

• chr22-34137753-C-T
• rs141418
• ENST00000412218.1:n.199-14112C>T

Variant summary

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

The NR_183585.1(LINC01643):​n.400-23843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.844 in 152,148 control chromosomes in the GnomAD database, including 54,697 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 (54697 hom., cov: 31)
• Consequence: LINC01643 NR_183585.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.949 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.400-23843C>T		intron	N/A
	LINC01643	NR_183586.1		n.240-23843C>T		intron	N/A
	LINC01643	NR_183587.1		n.348+28319C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01643	ENST00000412218.1	TSL:5	n.199-14112C>T		intron	N/A
	LINC01643	ENST00000652942.1		n.246-23843C>T		intron	N/A
	LINC01643	ENST00000653369.1		n.115-33960C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.844 AC: 128314 AN: 152030 Hom.: 54632 Cov.: 31

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.825

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.742

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.844 AC: 128438 AN: 152148 Hom.: 54697 Cov.: 31 AF XY: 0.847 AC XY: 63039 AN XY: 74384

African (AFR) AF: 0.957 AC: 39759 AN: 41538

American (AMR) AF: 0.816 AC: 12474 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.825 AC: 2865 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4629 AN: 5164

South Asian (SAS) AF: 0.903 AC: 4351 AN: 4820

European-Finnish (FIN) AF: 0.802 AC: 8477 AN: 10570

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.784 AC: 53281 AN: 67992

Other (OTH) AF: 0.833 AC: 1757 AN: 2110

Alfa AF: 0.825 Hom.: 6743

Bravo AF: 0.848

Asia WGS AF: 0.908 AC: 3155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.0
DANN	Benign	0.56
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs141418; hg19: chr22-34533742;