rs957794

Positions:

• chr21-45338851-G-C

Variant summary

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

The NR_103811.1(LINC00316):​n.194C>G 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 0.126 in 152,250 control chromosomes in the GnomAD database, including 1,347 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 0.13 (1347 hom., cov: 33)
  • Exomes 𝑓: 0.091 (0 hom.)
• Consequence: LINC00316 NR_103811.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00316	NR_103811.1	n.194C>G		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00316	ENST00000416722.1	n.194C>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19137 AN: 152110 Hom.: 1330 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.0896

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.124

GnomAD4 exome AF: 0.0909 AC: 2 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.111 AC XY: 2 AN XY: 18

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0714

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.126 AC: 19193 AN: 152228 Hom.: 1347 Cov.: 33 AF XY: 0.126 AC XY: 9390 AN XY: 74444

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.0896

Gnomad4 EAS AF: 0.0608

Gnomad4 SAS AF: 0.0794

Gnomad4 FIN AF: 0.120

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0571 Hom.: 51

Bravo AF: 0.132

Asia WGS AF: 0.0890 AC: 310 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	0.63
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs957794; hg19: chr21-46758766;