chr21-45338804-G-A

Position:

• chr21-45338804-G-A

Variant summary

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

The NR_103811.1(LINC00316):​n.241C>T 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 0.119 in 152,284 control chromosomes in the GnomAD database, including 1,176 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 0.12 (1176 hom., cov: 33)
  • Exomes 𝑓: 0.063 (0 hom.)
• Consequence: LINC00316 NR_103811.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

Genes affected

LINC00316 (HGNC:19723): (long intergenic non-protein coding RNA 316)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00316	NR_103811.1	n.241C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00316	ENST00000416722.1	n.241C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18011 AN: 152150 Hom.: 1160 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.0602

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.118

GnomAD4 exome AF: 0.0625 AC: 1 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.119 AC: 18065 AN: 152268 Hom.: 1176 Cov.: 33 AF XY: 0.119 AC XY: 8845 AN XY: 74476

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.0606

Gnomad4 SAS AF: 0.0796

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.116

Alfa AF: 0.107 Hom.: 896

Bravo AF: 0.123

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957795; hg19: chr21-46758719; COSMIC: COSV101395731;