rs1005932

Variant names:

• chr2-176466982-A-G
• rs1005932
• ENST00000814385.1:n.87+954A>G

Variant summary

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

The ENST00000814385.1(LINC01117):​n.87+954A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,108 control chromosomes in the GnomAD database, including 8,606 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 0.31 (8606 hom., cov: 32)
• Consequence: LINC01117 ENST00000814385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 5 publications found

Genes affected

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814385.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01117	ENST00000814385.1		n.87+954A>G		intron	N/A
	LINC01117	ENST00000814386.1		n.147+19902A>G		intron	N/A
	LINC01117	ENST00000814387.1		n.79+954A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46877 AN: 151990 Hom.: 8586 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.308 AC: 46909 AN: 152108 Hom.: 8606 Cov.: 32 AF XY: 0.313 AC XY: 23247 AN XY: 74346

African (AFR) AF: 0.144 AC: 5986 AN: 41510

American (AMR) AF: 0.500 AC: 7644 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 838 AN: 3472

East Asian (EAS) AF: 0.628 AC: 3240 AN: 5156

South Asian (SAS) AF: 0.349 AC: 1683 AN: 4816

European-Finnish (FIN) AF: 0.354 AC: 3745 AN: 10568

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22912 AN: 67990

Other (OTH) AF: 0.310 AC: 652 AN: 2104

Alfa AF: 0.332 Hom.: 30288

Bravo AF: 0.313

Asia WGS AF: 0.457 AC: 1589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	10
DANN	Benign	0.76
PhyloP100		1.3

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: rs1005932;

hg19: chr2-177331710;