18-42363228-C-T

Position:

• chr18-42363228-C-T

Variant summary

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

The NR_046174.2(LINC00907):​n.622+27925C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,032 control chromosomes in the GnomAD database, including 14,727 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 0.39 (14727 hom., cov: 33)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.622+27925C>T		intron_variant, non_coding_transcript_variant
LINC00907	NR_046454.1	n.403-90704C>T		intron_variant, non_coding_transcript_variant
LINC00907	NR_046456.1	n.713+27925C>T		intron_variant, non_coding_transcript_variant
LINC00907	NR_046457.1	n.493+73634C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000589068.5	n.587+27925C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59923 AN: 151912 Hom.: 14718 Cov.: 33

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.394 AC: 59936 AN: 152032 Hom.: 14727 Cov.: 33 AF XY: 0.394 AC XY: 29246 AN XY: 74298

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.420

Alfa AF: 0.494 Hom.: 10443

Bravo AF: 0.373

Asia WGS AF: 0.337 AC: 1173 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.036
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1461710; hg19: chr18-39943193;