rs326656

Variant names:

• chr1-96315001-T-A
• rs326656
• ENST00000435311.1:n.166-10663A>T

Variant summary

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

The ENST00000435311.1(LINC01787):​n.166-10663A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,000 control chromosomes in the GnomAD database, including 1,127 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 0.12 (1127 hom., cov: 32)
• Consequence: LINC01787 ENST00000435311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 3 publications found

Genes affected

LINC01787 (HGNC:52576): (long intergenic non-protein coding RNA 1787)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435311.1. 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
	LINC01787	NR_110693.1		n.166-10663A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01787	ENST00000435311.1	TSL:2	n.166-10663A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17892 AN: 151882 Hom.: 1130 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0802

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.118 AC: 17888 AN: 152000 Hom.: 1127 Cov.: 32 AF XY: 0.116 AC XY: 8594 AN XY: 74320

African (AFR) AF: 0.130 AC: 5406 AN: 41472

American (AMR) AF: 0.102 AC: 1545 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5186

South Asian (SAS) AF: 0.169 AC: 815 AN: 4818

European-Finnish (FIN) AF: 0.0802 AC: 850 AN: 10604

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8161 AN: 67922

Other (OTH) AF: 0.129 AC: 272 AN: 2110

Alfa AF: 0.115 Hom.: 119

Bravo AF: 0.119

Asia WGS AF: 0.0770 AC: 269 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.0030
DANN	Benign	0.12
PhyloP100		-0.48
Mutation Taster		=100/0	polymorphism

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: rs326656;

hg19: chr1-96780557;