rs9870410

Variant names:

• chr3-30267268-C-T
• rs9870410

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 0.0776 in 152,222 control chromosomes in the GnomAD database, including 581 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 0.078 (581 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 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: 0.0777 AC: 11811 AN: 152104 Hom.: 580 Cov.: 33

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0598

Gnomad FIN AF: 0.0938

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0776 AC: 11818 AN: 152222 Hom.: 581 Cov.: 33 AF XY: 0.0788 AC XY: 5861 AN XY: 74418

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0547

Gnomad4 ASJ AF: 0.0972

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0597

Gnomad4 FIN AF: 0.0938

Gnomad4 NFE AF: 0.0501

Gnomad4 OTH AF: 0.0780

Alfa AF: 0.0578 Hom.: 389

Bravo AF: 0.0775

Asia WGS AF: 0.0470 AC: 162 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9870410; hg19: chr3-30308759;