3-64087196-G-A

Position:

• chr3-64087196-G-A

Variant summary

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

The NR_033978.1(LINC00994):​n.168C>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 0.332 in 152,424 control chromosomes in the GnomAD database, including 8,893 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 0.33 (8855 hom., cov: 33)
  • Exomes 𝑓: 0.36 (38 hom.)
• Consequence: LINC00994 NR_033978.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.231

Genes affected

LINC00994 (HGNC:48949): (long intergenic non-protein coding RNA 994)

PRICKLE2-AS1 (HGNC:40916): (PRICKLE2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00994	NR_033978.1	n.168C>T		non_coding_transcript_exon_variant	1/4
PRICKLE2-AS1	NR_045697.1	n.199-7898G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00994	ENST00000485805.1	n.168C>T		non_coding_transcript_exon_variant	1/4	2
PRICKLE2-AS1	ENST00000482609.1	n.199-7898G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50290 AN: 151684 Hom.: 8839 Cov.: 33

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.365 AC: 227 AN: 622 Hom.: 38 Cov.: 0 AF XY: 0.374 AC XY: 131 AN XY: 350

Gnomad4 AFR exome AF: 0.00

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.360

Gnomad4 NFE exome AF: 0.367

Gnomad4 OTH exome AF: 0.425

GnomAD4 genome AF: 0.332 AC: 50328 AN: 151802 Hom.: 8855 Cov.: 33 AF XY: 0.339 AC XY: 25168 AN XY: 74200

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.341

Alfa AF: 0.341 Hom.: 12361

Bravo AF: 0.325

Asia WGS AF: 0.445 AC: 1549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.52
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs254855; hg19: chr3-64072872;