rs1887427

Variant names:

• chr9-4979730-A-G
• rs1887427

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.113 AC: 4709 AN: 41496

American (AMR) AF: 0.224 AC: 3416 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3468

East Asian (EAS) AF: 0.164 AC: 847 AN: 5162

South Asian (SAS) AF: 0.179 AC: 864 AN: 4824

European-Finnish (FIN) AF: 0.244 AC: 2576 AN: 10536

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17402 AN: 67952

Other (OTH) AF: 0.237 AC: 498 AN: 2102

Alfa AF: 0.238 Hom.: 11682

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
PhyloP100		0.43

Splicing

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

Other links and lift over

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