rs9870410

Positions:

• chr3-30267268-C-T

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;