rs593418

Positions:

• chr18-68261994-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183524.1(LINC01912):​n.1306-324A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 151,758 control chromosomes in the GnomAD database, including 28,837 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 0.61 (28837 hom., cov: 31)
• Consequence: LINC01912 NR_183524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

Genes affected

LINC01912 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01912	NR_183524.1	n.1306-324A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01912	ENST00000581844.1	n.130-324A>G		intron_variant		5
LINC01912	ENST00000657287.1	n.738-324A>G		intron_variant
ENSG00000287907	ENST00000661028.1	n.319-21852A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93080 AN: 151640 Hom.: 28808 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.614 AC: 93156 AN: 151758 Hom.: 28837 Cov.: 31 AF XY: 0.616 AC XY: 45636 AN XY: 74120

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.623

Alfa AF: 0.637 Hom.: 62090

Bravo AF: 0.610

Asia WGS AF: 0.657 AC: 2286 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs593418; hg19: chr18-65929231;