rs57302454

chr8-23081148-G-C

Variant summary

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

The NR_038873.1(LOC286059):n.264+92G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 332,230 control chromosomes in the GnomAD database, including 1,950 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 0.10 (1539 hom., cov: 32)
  • Exomes 𝑓: 0.056 (411 hom.)
• Consequence: LOC286059 NR_038873.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.962

Genes affected

(HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC286059	NR_038873.1	n.264+92G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000501897.1	n.264+92G>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15781 AN: 152068 Hom.: 1538 Cov.: 32

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0550

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.0581

Gnomad SAS AF: 0.0824

Gnomad FIN AF: 0.0317

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0402

Gnomad OTH AF: 0.0809

GnomAD4 exome AF: 0.0558 AC: 10049 AN: 180044 Hom.: 411 Cov.: 0 AF XY: 0.0569 AC XY: 5855 AN XY: 102838

Gnomad4 AFR exome AF: 0.273

Gnomad4 AMR exome AF: 0.0316

Gnomad4 ASJ exome AF: 0.0436

Gnomad4 EAS exome AF: 0.0673

Gnomad4 SAS exome AF: 0.0849

Gnomad4 FIN exome AF: 0.0405

Gnomad4 NFE exome AF: 0.0446

Gnomad4 OTH exome AF: 0.0542

GnomAD4 genome AF: 0.104 AC: 15802 AN: 152186 Hom.: 1539 Cov.: 32 AF XY: 0.102 AC XY: 7570 AN XY: 74418

Gnomad4 AFR AF: 0.261

Gnomad4 AMR AF: 0.0549

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.0580

Gnomad4 SAS AF: 0.0828

Gnomad4 FIN AF: 0.0317

Gnomad4 NFE AF: 0.0401

Gnomad4 OTH AF: 0.0801

Alfa AF: 0.0760 Hom.: 129

Bravo AF: 0.111

Asia WGS AF: 0.0780 AC: 271 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	0.18
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57302454; hg19: chr8-22938661; COSMIC: COSV67166642;