chr18-42333215-G-A

Variant names:

• chr18-42333215-G-A
• rs8095186
• ENST00000585627.5:n.239+107108G>A

Variant summary

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

The ENST00000585627.5(LINC00907):​n.239+107108G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.893 in 150,184 control chromosomes in the GnomAD database, including 59,904 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 0.89 (59904 hom., cov: 25)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.403-1869G>A		intron_variant	Intron 3 of 9
LINC00907	NR_046454.1	n.402+107108G>A		intron_variant	Intron 3 of 6
LINC00907	NR_046456.1	n.494-1869G>A		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.239+107108G>A		intron_variant	Intron 2 of 4	1
LINC00907	ENST00000585639.5	n.381+107108G>A		intron_variant	Intron 3 of 6	1
LINC00907	ENST00000586990.6	n.650-1869G>A		intron_variant	Intron 3 of 4	1

Frequencies

GnomAD3 genomes AF: 0.892 AC: 133923 AN: 150074 Hom.: 59833 Cov.: 25

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.893 AC: 134052 AN: 150184 Hom.: 59904 Cov.: 25 AF XY: 0.891 AC XY: 65102 AN XY: 73102

African (AFR) AF: 0.856 AC: 34851 AN: 40714

American (AMR) AF: 0.937 AC: 14043 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.960 AC: 3331 AN: 3470

East Asian (EAS) AF: 0.828 AC: 4177 AN: 5044

South Asian (SAS) AF: 0.840 AC: 3980 AN: 4740

European-Finnish (FIN) AF: 0.889 AC: 8910 AN: 10018

Middle Eastern (MID) AF: 0.959 AC: 280 AN: 292

European-Non Finnish (NFE) AF: 0.908 AC: 61687 AN: 67920

Other (OTH) AF: 0.911 AC: 1905 AN: 2090

Alfa AF: 0.908 Hom.: 105981

Bravo AF: 0.896

Asia WGS AF: 0.847 AC: 2947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.55
DANN	Benign	0.61
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs8095186; hg19: chr18-39913180;