rs2203858

chr15-21293860-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_027053.2(LOC646214):n.3970A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.30 (2 hom., cov: 0)
  • Exomes 𝑓: 0.34 (34 hom.)
  • Failed GnomAD Quality Control
• Consequence: LOC646214 NR_027053.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC646214	NR_027053.2	n.3970A>G		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000556425.2	n.1342A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 697 AN: 2306 Hom.: 2 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.167

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.273

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.342 AC: 25257 AN: 73746 Hom.: 34 Cov.: 0 AF XY: 0.343 AC XY: 12844 AN XY: 37500

Gnomad4 AFR exome AF: 0.336

Gnomad4 AMR exome AF: 0.299

Gnomad4 ASJ exome AF: 0.319

Gnomad4 EAS exome AF: 0.383

Gnomad4 SAS exome AF: 0.332

Gnomad4 FIN exome AF: 0.401

Gnomad4 NFE exome AF: 0.336

Gnomad4 OTH exome AF: 0.339

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.303 AC: 695 AN: 2292 Hom.: 2 Cov.: 0 AF XY: 0.296 AC XY: 302 AN XY: 1020

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.318

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.273

Alfa AF: 0.251 Hom.: 38

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	18
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2203858; hg19: chr15-21936770; COSMIC: COSV70888071;