rs1875189

Positions:

• chr5-174368789-A-G
• chr5-174368789-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_125806.1(LINC01411):​n.223+32213A>G variant causes a intron, non coding transcript 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 NR_125806.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01411	NR_125806.1	n.223+32213A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01411	ENST00000507361.5	n.223+32213A>G		intron_variant, non_coding_transcript_variant		3
LINC01411	ENST00000510234.5	n.82+32213A>G		intron_variant, non_coding_transcript_variant		3
LINC01411	ENST00000515513.5	n.282+32213A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.808

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.694

Alfa AF: 0.667 Hom.: 30404

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1875189; hg19: chr5-173795792;