13-100940866-C-G

Variant names:

• chr13-100940866-C-G
• rs3825523
• ENST00000657351.1:n.158G>C

Variant summary

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

The ENST00000657351.1(LINC00411):​n.158G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,242 control chromosomes in the GnomAD database, including 44,279 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 0.75 (44274 hom., cov: 33)
  • Exomes 𝑓: 0.81 (5 hom.)
• Consequence: LINC00411 ENST00000657351.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 3 publications found

Genes affected

LINC00411 (HGNC:42744): (long intergenic non-protein coding RNA 411)

NALCN-AS1 (HGNC:42743): (NALCN antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657351.1. 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
	LINC00411	NR_047015.1		n.321+136G>C		intron	N/A
	NALCN-AS1	NR_047687.1		n.142-72352C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00411	ENST00000657351.1		n.158G>C		non_coding_transcript_exon	Exon 1 of 2
	LINC00411	ENST00000667834.1		n.646G>C		non_coding_transcript_exon	Exon 2 of 3
	LINC00411	ENST00000436722.3	TSL:3	n.482+136G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114771 AN: 152108 Hom.: 44218 Cov.: 33

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.724

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.747

GnomAD4 exome AF: 0.813 AC: 13 AN: 16 Hom.: 5 Cov.: 0 AF XY: 0.786 AC XY: 11 AN XY: 14

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.917 AC: 11 AN: 12

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.755 AC: 114884 AN: 152226 Hom.: 44274 Cov.: 33 AF XY: 0.756 AC XY: 56265 AN XY: 74410

African (AFR) AF: 0.914 AC: 37975 AN: 41568

American (AMR) AF: 0.796 AC: 12178 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2180 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4054 AN: 5172

South Asian (SAS) AF: 0.677 AC: 3268 AN: 4824

European-Finnish (FIN) AF: 0.724 AC: 7659 AN: 10578

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45154 AN: 67996

Other (OTH) AF: 0.747 AC: 1577 AN: 2112

Alfa AF: 0.714 Hom.: 4605

Bravo AF: 0.770

Asia WGS AF: 0.758 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs3825523; hg19: chr13-101593120;