rs9953717

Variant names:

• chr18-71576503-T-C
• rs9953717
• ENST00000568095.5:n.150+2304A>G

Variant summary

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

The ENST00000568095.5(LINC01541):​n.150+2304A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 152,170 control chromosomes in the GnomAD database, including 54,050 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 0.84 (54050 hom., cov: 33)
• Consequence: LINC01541 ENST00000568095.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 2 publications found

Genes affected

LINC01541 (HGNC:51309): (long intergenic non-protein coding RNA 1541)

ENSG00000298599 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568095.5. 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
	LINC01541	NR_038325.1		n.150+2304A>G		intron	N/A
	LINC01541	NR_038326.1		n.150+2304A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01541	ENST00000568095.5	TSL:1	n.150+2304A>G		intron	N/A
	LINC01541	ENST00000566582.1	TSL:2	n.131+2304A>G		intron	N/A
	ENSG00000298599	ENST00000756734.1		n.181+28448T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127902 AN: 152052 Hom.: 54037 Cov.: 33

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.841

Gnomad ASJ AF: 0.893

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.846

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

GnomAD4 genome AF: 0.841 AC: 127967 AN: 152170 Hom.: 54050 Cov.: 33 AF XY: 0.843 AC XY: 62723 AN XY: 74390

African (AFR) AF: 0.770 AC: 31939 AN: 41484

American (AMR) AF: 0.840 AC: 12847 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.893 AC: 3096 AN: 3468

East Asian (EAS) AF: 0.906 AC: 4701 AN: 5186

South Asian (SAS) AF: 0.930 AC: 4488 AN: 4828

European-Finnish (FIN) AF: 0.878 AC: 9298 AN: 10596

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58874 AN: 68008

Other (OTH) AF: 0.839 AC: 1771 AN: 2110

Alfa AF: 0.862 Hom.: 25912

Bravo AF: 0.834

Asia WGS AF: 0.906 AC: 3145 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.50
DANN	Benign	0.38
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs9953717; hg19: chr18-69243739;