rs9304270

Variant names:

• chr18-42357544-C-T
• rs9304270
• ENST00000585627.5:n.240-96388C>T

Variant summary

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

The ENST00000585627.5(LINC00907):​n.240-96388C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 151,632 control chromosomes in the GnomAD database, including 3,178 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 0.19 (3178 hom., cov: 31)
• Consequence: LINC00907 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 7 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000585627.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00907	NR_046174.2		n.622+22241C>T		intron	N/A
	LINC00907	NR_046454.1		n.403-96388C>T		intron	N/A
	LINC00907	NR_046456.1		n.713+22241C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00907	ENST00000585627.5	TSL:1	n.240-96388C>T		intron	N/A
	LINC00907	ENST00000585639.5	TSL:1	n.382-96388C>T		intron	N/A
	LINC00907	ENST00000591381.5	TSL:1	n.223-96388C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28714 AN: 151524 Hom.: 3164 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.190 AC: 28777 AN: 151632 Hom.: 3178 Cov.: 31 AF XY: 0.189 AC XY: 14000 AN XY: 74022

African (AFR) AF: 0.297 AC: 12269 AN: 41358

American (AMR) AF: 0.159 AC: 2423 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 596 AN: 3466

East Asian (EAS) AF: 0.373 AC: 1923 AN: 5154

South Asian (SAS) AF: 0.178 AC: 852 AN: 4786

European-Finnish (FIN) AF: 0.119 AC: 1232 AN: 10382

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8885 AN: 67952

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.157 Hom.: 5752

Bravo AF: 0.200

Asia WGS AF: 0.294 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.87
DANN	Benign	0.44
PhyloP100		-1.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9304270;

hg19: chr18-39937509;