rs297903

Variant names:

• chr12-49915969-G-A
• rs297903
• ENST00000546821.5:n.131+3886G>A

Variant summary

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

The ENST00000546821.5(LINC02395):​n.131+3886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.029 in 152,080 control chromosomes in the GnomAD database, including 191 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 0.029 (191 hom., cov: 32)
• Consequence: LINC02395 ENST00000546821.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 1 publications found

Genes affected

LINC02395 (HGNC:53322): (long intergenic non-protein coding RNA 2395)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546821.5. 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
	LINC02395	NR_110048.1		n.131+3886G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02395	ENST00000546821.5	TSL:1	n.131+3886G>A		intron	N/A
	LINC02395	ENST00000547954.2	TSL:3	n.407-7656G>A		intron	N/A
	LINC02395	ENST00000549734.1	TSL:4	n.104+3886G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0290 AC: 4412 AN: 151964 Hom.: 192 Cov.: 32

Gnomad AFR AF: 0.0990

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000415

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00641

Gnomad NFE AF: 0.000441

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0290 AC: 4415 AN: 152080 Hom.: 191 Cov.: 32 AF XY: 0.0284 AC XY: 2109 AN XY: 74358

African (AFR) AF: 0.0988 AC: 4098 AN: 41468

American (AMR) AF: 0.0150 AC: 230 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000415 AC: 2 AN: 4818

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10562

Middle Eastern (MID) AF: 0.00690 AC: 2 AN: 290

European-Non Finnish (NFE) AF: 0.000441 AC: 30 AN: 67980

Other (OTH) AF: 0.0242 AC: 51 AN: 2110

Alfa AF: 0.0247 Hom.: 18

Bravo AF: 0.0342

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.97
DANN	Benign	0.30
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: rs297903;

hg19: chr12-50309752;