rs9311032

Positions:

• chr3-33873113-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 64 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0457

Gnomad4 AMR AF: 0.0210

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.0181

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.0469

Gnomad4 NFE AF: 0.0172

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0213 Hom.: 6

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9311032; hg19: chr3-33914605;