chr5-174367153-A-G

Variant names:

• chr5-174367153-A-G
• rs2964115
• ENST00000507361.5:n.223+30577A>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+30577A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,048 control chromosomes in the GnomAD database, including 54,346 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 0.85 (54346 hom., cov: 30)
• Consequence: LINC01411 ENST00000507361.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 3 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507361.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01411	NR_125806.1		n.223+30577A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01411	ENST00000507361.5	TSL:3	n.223+30577A>G		intron	N/A
	LINC01411	ENST00000510234.6	TSL:3	n.185+30577A>G		intron	N/A
	LINC01411	ENST00000515513.5	TSL:5	n.282+30577A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128402 AN: 151930 Hom.: 54289 Cov.: 30

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.952

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.845 AC: 128517 AN: 152048 Hom.: 54346 Cov.: 30 AF XY: 0.844 AC XY: 62731 AN XY: 74288

African (AFR) AF: 0.880 AC: 36498 AN: 41470

American (AMR) AF: 0.840 AC: 12835 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3016 AN: 3470

East Asian (EAS) AF: 0.952 AC: 4910 AN: 5158

South Asian (SAS) AF: 0.764 AC: 3679 AN: 4816

European-Finnish (FIN) AF: 0.854 AC: 9001 AN: 10544

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.821 AC: 55808 AN: 68004

Other (OTH) AF: 0.874 AC: 1839 AN: 2104

Alfa AF: 0.831 Hom.: 86175

Bravo AF: 0.849

Asia WGS AF: 0.848 AC: 2949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.19
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs2964115; hg19: chr5-173794156;