rs9311032

Variant names:

• chr3-33873113-C-T
• rs9311032

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0276 in 152,356 control chromosomes in the GnomAD database, including 64 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 0.028 (64 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0276 (4202/152356) while in subpopulation AFR AF = 0.0457 (1898/41576). AF 95% confidence interval is 0.0439. There are 64 homozygotes in GnomAd4. There are 2146 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 64 gene

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: 0.0276 AC: 4199 AN: 152238 Hom.: 64 Cov.: 33

Gnomad AFR AF: 0.0457

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0209

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.0182

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0172

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0276 AC: 4202 AN: 152356 Hom.: 64 Cov.: 33 AF XY: 0.0288 AC XY: 2146 AN XY: 74504

African (AFR) AF: 0.0457 AC: 1898 AN: 41576

American (AMR) AF: 0.0210 AC: 321 AN: 15312

Ashkenazi Jewish (ASJ) AF: 0.00778 AC: 27 AN: 3472

East Asian (EAS) AF: 0.0181 AC: 94 AN: 5194

South Asian (SAS) AF: 0.0263 AC: 127 AN: 4826

European-Finnish (FIN) AF: 0.0469 AC: 498 AN: 10618

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0172 AC: 1168 AN: 68038

Other (OTH) AF: 0.0232 AC: 49 AN: 2114

Alfa AF: 0.0221 Hom.: 7

Bravo AF: 0.0264

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.82
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs9311032; hg19: chr3-33914605;