rs346452

Variant names:

• chr18-42361001-G-A
• rs346452
• ENST00000585627.5:n.240-92931G>A

Variant summary

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

The ENST00000585627.5(LINC00907):​n.240-92931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 151,966 control chromosomes in the GnomAD database, including 11,387 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 0.38 (11387 hom., cov: 32)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 2 publications found

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

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 (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585627.5. 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
	LINC00907	NR_046174.2		n.622+25698G>A		intron	N/A
	LINC00907	NR_046454.1		n.403-92931G>A		intron	N/A
	LINC00907	NR_046456.1		n.713+25698G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00907	ENST00000585627.5	TSL:1	n.240-92931G>A		intron	N/A
	LINC00907	ENST00000585639.5	TSL:1	n.382-92931G>A		intron	N/A
	LINC00907	ENST00000591381.5	TSL:1	n.223-92931G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57861 AN: 151850 Hom.: 11368 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.381 AC: 57932 AN: 151966 Hom.: 11387 Cov.: 32 AF XY: 0.384 AC XY: 28510 AN XY: 74250

African (AFR) AF: 0.413 AC: 17112 AN: 41472

American (AMR) AF: 0.413 AC: 6304 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3468

East Asian (EAS) AF: 0.685 AC: 3529 AN: 5154

South Asian (SAS) AF: 0.275 AC: 1323 AN: 4818

European-Finnish (FIN) AF: 0.367 AC: 3871 AN: 10558

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23402 AN: 67930

Other (OTH) AF: 0.399 AC: 841 AN: 2110

Alfa AF: 0.385 Hom.: 4742

Bravo AF: 0.391

Asia WGS AF: 0.491 AC: 1703 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.66
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs346452; hg19: chr18-39940966;