rs1389158

Variant names:

• chr21-17442107-A-G
• rs1389158
• ENST00000440664.7:n.363+264A>G

Variant summary

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

The ENST00000440664.7(LINC01549):​n.363+264A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 152,252 control chromosomes in the GnomAD database, including 352 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 0.042 (352 hom., cov: 32)
• Consequence: LINC01549 ENST00000440664.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 1 publications found

Genes affected

LINC01549 (HGNC:1277): (long intergenic non-protein coding RNA 1549)

ENSG00000296104 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440664.7. 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
	LINC01549	NR_037585.1		n.278+264A>G		intron	N/A
	LINC01549	NR_037586.1		n.278+264A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01549	ENST00000440664.7	TSL:3	n.363+264A>G		intron	N/A
	LINC01549	ENST00000613691.1	TSL:5	n.63+264A>G		intron	N/A
	ENSG00000296104	ENST00000736448.1		n.76+4628T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6314 AN: 152134 Hom.: 352 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00393

Gnomad FIN AF: 0.00414

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0415 AC: 6321 AN: 152252 Hom.: 352 Cov.: 32 AF XY: 0.0405 AC XY: 3016 AN XY: 74440

African (AFR) AF: 0.123 AC: 5108 AN: 41516

American (AMR) AF: 0.0194 AC: 297 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0161 AC: 56 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00414 AC: 20 AN: 4826

European-Finnish (FIN) AF: 0.00414 AC: 44 AN: 10616

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0102 AC: 696 AN: 68028

Other (OTH) AF: 0.0388 AC: 82 AN: 2114

Alfa AF: 0.0231 Hom.: 51

Bravo AF: 0.0466

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.6
DANN	Benign	0.77
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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: rs1389158;

hg19: chr21-18814425;