13-100940866-C-G

Position:

• chr13-100940866-C-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC00411 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00411	NR_047015.1	n.321+136G>C		intron_variant
NALCN-AS1	NR_047687.1	n.142-72352C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00411	ENST00000657351.1	n.158G>C		non_coding_transcript_exon_variant	1/2
LINC00411	ENST00000667834.1	n.646G>C		non_coding_transcript_exon_variant	2/3
LINC00411	ENST00000436722.2	n.471+136G>C		intron_variant		3
NALCN-AS1	ENST00000457843.1	n.142-72352C>G		intron_variant		2

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

Gnomad4 AFR exome AF: 0.500

Gnomad4 NFE exome AF: 0.917

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.724

Gnomad4 NFE AF: 0.664

Gnomad4 OTH AF: 0.747

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3825523; hg19: chr13-101593120;