rs504390

Variant names:

• chr1-170191980-C-A
• rs504390
• ENST00000439184.1:n.304+17274C>A

Variant summary

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

The ENST00000439184.1(LINC01681):​n.304+17274C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,184 control chromosomes in the GnomAD database, including 3,079 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 0.17 (3079 hom., cov: 32)
• Consequence: LINC01681 ENST00000439184.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145
• Publications: 3 publications found

Genes affected

LINC01681 (HGNC:52468): (long intergenic non-protein coding RNA 1681)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439184.1. 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
	LINC01681	NR_146891.1		n.328+17274C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01681	ENST00000439184.1	TSL:2	n.304+17274C>A		intron	N/A
	LINC01681	ENST00000654877.1		n.320+17274C>A		intron	N/A
	LINC01681	ENST00000654909.1		n.340+17274C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26173 AN: 152066 Hom.: 3072 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.172 AC: 26197 AN: 152184 Hom.: 3079 Cov.: 32 AF XY: 0.176 AC XY: 13106 AN XY: 74400

African (AFR) AF: 0.0412 AC: 1712 AN: 41562

American (AMR) AF: 0.227 AC: 3471 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2904 AN: 5150

South Asian (SAS) AF: 0.145 AC: 698 AN: 4818

European-Finnish (FIN) AF: 0.214 AC: 2261 AN: 10590

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14138 AN: 67990

Other (OTH) AF: 0.197 AC: 417 AN: 2116

Alfa AF: 0.185 Hom.: 348

Bravo AF: 0.172

Asia WGS AF: 0.318 AC: 1102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.33
PhyloP100		0.14

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: rs504390;

hg19: chr1-170161121;