chr18-42363228-C-T

Variant names:

• chr18-42363228-C-T
• rs1461710
• ENST00000585627.5:n.240-90704C>T

Variant summary

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

The ENST00000585627.5(LINC00907):​n.240-90704C>T variant causes a intron 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 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 6 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=-0.93).
• 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 rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.622+27925C>T		intron_variant	Intron 4 of 9
LINC00907	NR_046454.1	n.403-90704C>T		intron_variant	Intron 3 of 6
LINC00907	NR_046456.1	n.713+27925C>T		intron_variant	Intron 5 of 7
LINC00907	NR_046457.1	n.493+73634C>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.240-90704C>T		intron_variant	Intron 2 of 4	1
LINC00907	ENST00000585639.5	n.382-90704C>T		intron_variant	Intron 3 of 6	1
LINC00907	ENST00000591381.5	n.223-90704C>T		intron_variant	Intron 2 of 4	1

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

African (AFR) AF: 0.101 AC: 4200 AN: 41484

American (AMR) AF: 0.452 AC: 6891 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2044 AN: 3470

East Asian (EAS) AF: 0.123 AC: 633 AN: 5162

South Asian (SAS) AF: 0.573 AC: 2766 AN: 4824

European-Finnish (FIN) AF: 0.504 AC: 5323 AN: 10554

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36480 AN: 67974

Other (OTH) AF: 0.420 AC: 885 AN: 2108

Alfa AF: 0.436 Hom.: 13956

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1461710; hg19: chr18-39943193;