rs8095186

Positions:

• chr18-42333215-G-A
• chr18-42333215-G-C
• chr18-42333215-G-T

Variant summary

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

The NR_046174.2(LINC00907):​n.403-1869G>A 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 0.893 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 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-0.94).
• 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/exons	MANE	UniProt
LINC00907	NR_046174.2	n.403-1869G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.368-1869G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.856

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.908

Gnomad4 OTH AF: 0.911

Alfa AF: 0.909 Hom.: 83646

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8095186; hg19: chr18-39913180;