rs9310803

Variant names:

• chr3-26432072-C-T
• rs9310803

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 0.15 in 150,124 control chromosomes in the GnomAD database, including 3,694 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 0.15 (3694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22509 AN: 150012 Hom.: 3683 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0816

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.0136

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.150 AC: 22553 AN: 150124 Hom.: 3694 Cov.: 32 AF XY: 0.146 AC XY: 10691 AN XY: 73258

African (AFR) AF: 0.412 AC: 16911 AN: 41050

American (AMR) AF: 0.0814 AC: 1224 AN: 15046

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 433 AN: 3448

East Asian (EAS) AF: 0.000197 AC: 1 AN: 5080

South Asian (SAS) AF: 0.0136 AC: 65 AN: 4782

European-Finnish (FIN) AF: 0.0487 AC: 489 AN: 10034

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.0463 AC: 3119 AN: 67392

Other (OTH) AF: 0.126 AC: 264 AN: 2090

Alfa AF: 0.118 Hom.: 365

Bravo AF: 0.164

Asia WGS AF: 0.0340 AC: 118 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.51
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs9310803; hg19: chr3-26473563;