rs16972414

Positions:

• chr18-39875958-A-G

Variant summary

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

The ENST00000636467.2(LINC01902):​n.5778A>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 0.244 in 151,786 control chromosomes in the GnomAD database, including 5,174 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 0.24 (5174 hom., cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01902 ENST00000636467.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

Genes affected

LINC01902 (HGNC:52721): (long intergenic non-protein coding RNA 1902)

LINC01901 (HGNC:52720): (long intergenic non-protein coding RNA 1901)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01902	NR_151703.1	n.822-430A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01902	ENST00000636467.2	n.5778A>G		non_coding_transcript_exon_variant	6/7	5
LINC01901	ENST00000585822.1	n.310+346T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37088 AN: 151668 Hom.: 5179 Cov.: 31

Gnomad AFR AF: 0.0965

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.259

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.244 AC: 37090 AN: 151786 Hom.: 5174 Cov.: 31 AF XY: 0.247 AC XY: 18284 AN XY: 74126

Gnomad4 AFR AF: 0.0965

Gnomad4 AMR AF: 0.283

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.261

Alfa AF: 0.256 Hom.: 1031

Bravo AF: 0.232

Asia WGS AF: 0.352 AC: 1222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.035
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16972414; hg19: chr18-37455922;