18-42268019-T-C

Variant names:

• chr18-42268019-T-C
• rs1461719
• ENST00000585627.5:n.239+41912T>C

Variant summary

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

The ENST00000585627.5(LINC00907):​n.239+41912T>C variant causes a intron 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 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• 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=-0.86).
• 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 rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.402+41912T>C		intron_variant	Intron 3 of 9
LINC00907	NR_046454.1	n.402+41912T>C		intron_variant	Intron 3 of 6
LINC00907	NR_046456.1	n.403-21485T>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.239+41912T>C		intron_variant	Intron 2 of 4	1
LINC00907	ENST00000585639.5	n.381+41912T>C		intron_variant	Intron 3 of 6	1
LINC00907	ENST00000586990.6	n.649+41912T>C		intron_variant	Intron 3 of 4	1

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

African (AFR) AF: 0.586 AC: 24250 AN: 41394

American (AMR) AF: 0.766 AC: 11696 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.721 AC: 2499 AN: 3468

East Asian (EAS) AF: 0.969 AC: 5012 AN: 5170

South Asian (SAS) AF: 0.837 AC: 4038 AN: 4822

European-Finnish (FIN) AF: 0.633 AC: 6654 AN: 10514

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.715 AC: 48606 AN: 67952

Other (OTH) AF: 0.681 AC: 1436 AN: 2108

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1461719; hg19: chr18-39847984;