rs297941

chr12-49925303-A-Gchr12-49925303-A-T

Variant summary

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

The NR_110048.1(LINC02395):n.2813A>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 0.537 in 152,134 control chromosomes in the GnomAD database, including 23,760 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 0.54 (23760 hom., cov: 32)
  • Exomes 𝑓: 0.31 (0 hom.)
• Consequence: LINC02395 NR_110048.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

LINC02395 (HGNC:53322): (long intergenic non-protein coding RNA 2395)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02395	NR_110048.1	n.2813A>G		non_coding_transcript_exon_variant	5/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02395	ENST00000657051.1	n.583+216A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81661 AN: 152000 Hom.: 23710 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.585

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.514

GnomAD4 exome AF: 0.313 AC: 5 AN: 16 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.537 AC: 81758 AN: 152118 Hom.: 23760 Cov.: 32 AF XY: 0.529 AC XY: 39322 AN XY: 74394

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.511

Alfa AF: 0.462 Hom.: 21458

Bravo AF: 0.553

Asia WGS AF: 0.468 AC: 1628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.14
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs297941; hg19: chr12-50319086;