rs1887427

chr9-4979730-A-G

Variant summary

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

The variant allele was found at a frequency of 0.209 in 152,024 control chromosomes in the GnomAD database, including 3,646 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 0.21 (3646 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 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

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31789 AN: 151906 Hom.: 3647 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.237

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.209 AC: 31793 AN: 152024 Hom.: 3646 Cov.: 32 AF XY: 0.208 AC XY: 15474 AN XY: 74316

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.237

Alfa AF: 0.242 Hom.: 4275

Bravo AF: 0.206

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.9
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1887427; hg19: chr9-4979730; COSMIC: COSV69444398;