rs9310223

Variant names:

• chr3-71847228-C-A
• rs9310223

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 0.831 in 152,194 control chromosomes in the GnomAD database, including 52,968 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 0.83 (52968 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.874 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: 0.831 AC: 126355 AN: 152076 Hom.: 52930 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.737

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.897

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.827

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

GnomAD4 genome AF: 0.831 AC: 126442 AN: 152194 Hom.: 52968 Cov.: 32 AF XY: 0.825 AC XY: 61374 AN XY: 74402

Gnomad4 AFR AF: 0.812

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.737

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.897

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.828

Alfa AF: 0.833 Hom.: 22529

Bravo AF: 0.814

Asia WGS AF: 0.791 AC: 2753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9310223; hg19: chr3-71896379;