rs141418

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr22-34137753-C-G
• chr22-34137753-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000412218.1(LINC01643):​n.199-14112C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: LINC01643 ENST00000412218.1 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01643	NR_183585.1	n.400-23843C>G		intron_variant	Intron 5 of 10
LINC01643	NR_183586.1	n.240-23843C>G		intron_variant	Intron 3 of 8
LINC01643	NR_183587.1	n.348+28319C>G		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01643	ENST00000412218.1	n.199-14112C>G		intron_variant	Intron 3 of 7	5
LINC01643	ENST00000652942.1	n.246-23843C>G		intron_variant	Intron 3 of 7
LINC01643	ENST00000653369.1	n.115-33960C>G		intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.48
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;