rs1461718

chr18-42270834-A-Gchr18-42270834-A-T

Variant summary

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

The NR_046174.2(LINC00907):n.402+44727A>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 0.81 in 152,074 control chromosomes in the GnomAD database, including 50,142 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 0.81 (50142 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC00907 NR_046174.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00907	NR_046174.2	n.402+44727A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00907	ENST00000589068.5	n.367+44727A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123174 AN: 151954 Hom.: 50114 Cov.: 31

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.947

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.769

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.799

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.810 AC: 123251 AN: 152072 Hom.: 50142 Cov.: 31 AF XY: 0.812 AC XY: 60354 AN XY: 74328

Gnomad4 AFR AF: 0.744

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.971

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.769

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.801

Alfa AF: 0.808 Hom.: 5847

Bravo AF: 0.815

Asia WGS AF: 0.923 AC: 3200 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1461718; hg19: chr18-39850799;