18-42268019-T-C

Position:

• chr18-42268019-T-C

Variant summary

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

The NR_046174.2(LINC00907):​n.402+41912T>C 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 0.693 in 151,894 control chromosomes in the GnomAD database, including 37,075 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 0.69 (37075 hom., cov: 31)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.402+41912T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.367+41912T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105161 AN: 151776 Hom.: 37052 Cov.: 31

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.889

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.721

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.693 AC: 105225 AN: 151894 Hom.: 37075 Cov.: 31 AF XY: 0.694 AC XY: 51527 AN XY: 74236

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.721

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.681

Alfa AF: 0.693 Hom.: 4588

Bravo AF: 0.700

Asia WGS AF: 0.882 AC: 3063 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.56
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1461719; hg19: chr18-39847984;