rs2187961

Variant names:

• chr22-35185406-G-A
• rs2187961
• ENST00000423311.1:n.222+9451C>T

Variant summary

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

The ENST00000423311.1(LINC01399):​n.222+9451C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0596 in 152,224 control chromosomes in the GnomAD database, including 361 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 0.060 (361 hom., cov: 33)
• Consequence: LINC01399 ENST00000423311.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 publications found

Genes affected

LINC01399 (HGNC:):

LINC01399 (HGNC:50680): (long intergenic non-protein coding RNA 1399)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423311.1. 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
	LINC01399	NR_126356.1		n.222+9451C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01399	ENST00000423311.1	TSL:3	n.222+9451C>T		intron	N/A
	LINC01399	ENST00000798716.1		n.63-12946C>T		intron	N/A
	LINC01399	ENST00000798717.1		n.222-2012C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0596 AC: 9060 AN: 152106 Hom.: 357 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0589

Gnomad ASJ AF: 0.0352

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.0232

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0370

Gnomad OTH AF: 0.0485

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

GnomAD4 genome AF: 0.0596 AC: 9077 AN: 152224 Hom.: 361 Cov.: 33 AF XY: 0.0590 AC XY: 4392 AN XY: 74430

African (AFR) AF: 0.102 AC: 4220 AN: 41524

American (AMR) AF: 0.0587 AC: 898 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0352 AC: 122 AN: 3470

East Asian (EAS) AF: 0.144 AC: 743 AN: 5176

South Asian (SAS) AF: 0.0466 AC: 225 AN: 4826

European-Finnish (FIN) AF: 0.0232 AC: 246 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0370 AC: 2519 AN: 68014

Other (OTH) AF: 0.0480 AC: 101 AN: 2106

Alfa AF: 0.0433 Hom.: 91

Bravo AF: 0.0621

Asia WGS AF: 0.0890 AC: 309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.23
PhyloP100		0.25

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: rs2187961;

hg19: chr22-35581399;