rs346452

Positions:

• chr18-42361001-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00907 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.622+25698G>A		intron_variant
LINC00907	NR_046454.1	n.403-92931G>A		intron_variant
LINC00907	NR_046456.1	n.713+25698G>A		intron_variant
LINC00907	NR_046457.1	n.493+71407G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.240-92931G>A		intron_variant		1
LINC00907	ENST00000585639.5	n.382-92931G>A		intron_variant		1
LINC00907	ENST00000591381.5	n.223-92931G>A		intron_variant		1

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

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.399

Alfa AF: 0.366 Hom.: 2154

Bravo AF: 0.391

Asia WGS AF: 0.491 AC: 1703 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs346452; hg19: chr18-39940966;