chr5-174368789-A-G

Variant names:

• chr5-174368789-A-G
• rs1875189
• ENST00000507361.5:n.223+32213A>G

Variant summary

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

The ENST00000507361.5(LINC01411):​n.223+32213A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,072 control chromosomes in the GnomAD database, including 37,432 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 0.70 (37432 hom., cov: 31)
• Consequence: LINC01411 ENST00000507361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 5 publications found

Genes affected

LINC01411 (HGNC:50703): (long intergenic non-protein coding RNA 1411)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01411	NR_125806.1	n.223+32213A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01411	ENST00000507361.5	n.223+32213A>G		intron_variant	Intron 1 of 3	3
LINC01411	ENST00000510234.6	n.185+32213A>G		intron_variant	Intron 2 of 6	3
LINC01411	ENST00000515513.5	n.282+32213A>G		intron_variant	Intron 1 of 4	5

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105763 AN: 151954 Hom.: 37383 Cov.: 31

Gnomad AFR AF: 0.808

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.696 AC: 105861 AN: 152072 Hom.: 37432 Cov.: 31 AF XY: 0.694 AC XY: 51562 AN XY: 74308

African (AFR) AF: 0.808 AC: 33536 AN: 41486

American (AMR) AF: 0.604 AC: 9222 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2463 AN: 3472

East Asian (EAS) AF: 0.517 AC: 2666 AN: 5154

South Asian (SAS) AF: 0.521 AC: 2504 AN: 4810

European-Finnish (FIN) AF: 0.771 AC: 8168 AN: 10596

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45102 AN: 67968

Other (OTH) AF: 0.694 AC: 1464 AN: 2110

Alfa AF: 0.673 Hom.: 41005

Bravo AF: 0.694

Asia WGS AF: 0.526 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.57
PhyloP100		-1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1875189; hg19: chr5-173795792;