rs4877406

chr9-88145890-C-T

Variant summary

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

The 9-88145890-C-T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,090 control chromosomes in the GnomAD database, including 7,084 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 0.30 (7077 hom., cov: 32)
  • Exomes 𝑓: 0.26 (7 hom.)
• Consequence: ENST00000614041.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000614041.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45539 AN: 151790 Hom.: 7066 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.261

GnomAD4 exome AF: 0.258 AC: 47 AN: 182 Hom.: 7 Cov.: 0 AF XY: 0.283 AC XY: 26 AN XY: 92

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.281

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.300 AC: 45594 AN: 151908 Hom.: 7077 Cov.: 32 AF XY: 0.305 AC XY: 22614 AN XY: 74228

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.265

Alfa AF: 0.274 Hom.: 7964

Bravo AF: 0.304

Asia WGS AF: 0.319 AC: 1105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.6
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4877406; hg19: chr9-90760805;