rs504390

chr1-170191980-C-A

Variant summary

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

The NR_146891.1(LINC01681):n.328+17274C>A 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 0.172 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 NR_146891.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01681	NR_146891.1	n.328+17274C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01681	ENST00000666308.1	n.342+17274C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0412

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.197

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	1.5
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs504390; hg19: chr1-170161121;