rs1461718

Variant names:

• chr18-42270834-A-G
• rs1461718
• ENST00000585627.5:n.239+44727A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-42270834-A-G
• chr18-42270834-A-T

Variant summary

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

The ENST00000585627.5(LINC00907):​n.239+44727A>G variant causes a intron 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 ENST00000585627.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 2 publications found

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

RNA5SP454 (HGNC:43354): (RNA, 5S ribosomal pseudogene 454)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00907	NR_046174.2	n.402+44727A>G		intron_variant	Intron 3 of 9
LINC00907	NR_046454.1	n.402+44727A>G		intron_variant	Intron 3 of 6
LINC00907	NR_046456.1	n.403-18670A>G		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00907	ENST00000585627.5	n.239+44727A>G		intron_variant	Intron 2 of 4	1
LINC00907	ENST00000585639.5	n.381+44727A>G		intron_variant	Intron 3 of 6	1
LINC00907	ENST00000586990.6	n.649+44727A>G		intron_variant	Intron 3 of 4	1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.744 AC: 30838 AN: 41468

American (AMR) AF: 0.850 AC: 12980 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2815 AN: 3472

East Asian (EAS) AF: 0.971 AC: 5021 AN: 5172

South Asian (SAS) AF: 0.901 AC: 4336 AN: 4812

European-Finnish (FIN) AF: 0.769 AC: 8116 AN: 10556

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

European-Non Finnish (NFE) AF: 0.828 AC: 56328 AN: 68008

Other (OTH) AF: 0.801 AC: 1692 AN: 2112

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
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1461718; hg19: chr18-39850799;