rs9953717

Positions:

• chr18-71576503-T-C

Variant summary

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

The NR_038326.1(LINC01541):​n.150+2304A>G 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 0.841 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 NR_038326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134

Genes affected

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

LOC107985179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01541	NR_038326.1	n.150+2304A>G		intron_variant, non_coding_transcript_variant
LOC107985179	XR_001753502.1	n.149+28448T>C		intron_variant, non_coding_transcript_variant
LINC01541	NR_038325.1	n.150+2304A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01541	ENST00000568095.5	n.150+2304A>G		intron_variant, non_coding_transcript_variant		1
LINC01541	ENST00000566582.1	n.131+2304A>G		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.893

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.930

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.866

Gnomad4 OTH AF: 0.839

Alfa AF: 0.863 Hom.: 23641

Bravo AF: 0.834

Asia WGS AF: 0.906 AC: 3145 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9953717; hg19: chr18-69243739;