rs2546890

chr5-159332892-A-G

Variant summary

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

The NR_037889.1(LOC285626):n.634A>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 0.523 in 151,980 control chromosomes in the GnomAD database, including 21,278 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 0.52 (21269 hom., cov: 31)
  • Exomes 𝑓: 0.55 (9 hom.)
• Consequence: LOC285626 NR_037889.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC285626	NR_037889.1	n.634A>G		non_coding_transcript_exon_variant	2/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000515337.1	n.634A>G		non_coding_transcript_exon_variant	2/5	2
	ENST00000521472.6	n.521A>G		non_coding_transcript_exon_variant	4/4	3
	ENST00000641150.1	n.213A>G		non_coding_transcript_exon_variant	2/5

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79354 AN: 151806 Hom.: 21251 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.551

GnomAD4 exome AF: 0.554 AC: 31 AN: 56 Hom.: 9 Cov.: 0 AF XY: 0.438 AC XY: 14 AN XY: 32

Gnomad4 AMR exome AF: 0.750

Gnomad4 EAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.528

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.523 AC: 79408 AN: 151924 Hom.: 21269 Cov.: 31 AF XY: 0.518 AC XY: 38451 AN XY: 74240

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.551

Alfa AF: 0.499 Hom.: 44349

Bravo AF: 0.546

Asia WGS AF: 0.544 AC: 1891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.33
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2546890; hg19: chr5-158759900;