rs225553

Variant names:

• chr12-125949716-C-A
• rs225553
• ENST00000822064.1:n.484-5469G>T

Your query was ambiguous. Multiple possible variants found:

• chr12-125949716-C-A
• chr12-125949716-C-T

Variant summary

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

The ENST00000822064.1(LINC00939):​n.484-5469G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0996 in 152,226 control chromosomes in the GnomAD database, including 834 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 0.10 (834 hom., cov: 32)
• Consequence: LINC00939 ENST00000822064.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 2 publications found

Genes affected

LINC00939 (HGNC:48631): (long intergenic non-protein coding RNA 939)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822064.1. 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
	LINC00939	ENST00000822064.1		n.484-5469G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15139 AN: 152108 Hom.: 830 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.0996 AC: 15166 AN: 152226 Hom.: 834 Cov.: 32 AF XY: 0.0969 AC XY: 7215 AN XY: 74430

African (AFR) AF: 0.143 AC: 5948 AN: 41526

American (AMR) AF: 0.0974 AC: 1490 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.0705 AC: 365 AN: 5178

South Asian (SAS) AF: 0.0757 AC: 366 AN: 4834

European-Finnish (FIN) AF: 0.0335 AC: 355 AN: 10606

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0878 AC: 5971 AN: 67992

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.0875 Hom.: 312

Bravo AF: 0.107

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.56
PhyloP100		0.18

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: rs225553;

hg19: chr12-126434262;