rs305520

Variant names:

• chr3-11975083-G-A
• rs305520

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 0.0284 in 152,280 control chromosomes in the GnomAD database, including 73 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 (73 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0284 (4323/152280) while in subpopulation EAS AF = 0.0455 (236/5184). AF 95% confidence interval is 0.0408. There are 73 homozygotes in GnomAd4. There are 2166 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 73 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0284 AC: 4319 AN: 152162 Hom.: 73 Cov.: 32

Gnomad AFR AF: 0.00618

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0345

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.0454

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0419

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0358

Gnomad OTH AF: 0.0397

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

GnomAD4 genome AF: 0.0284 AC: 4323 AN: 152280 Hom.: 73 Cov.: 32 AF XY: 0.0291 AC XY: 2166 AN XY: 74468

African (AFR) AF: 0.00616 AC: 256 AN: 41552

American (AMR) AF: 0.0344 AC: 527 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0276 AC: 96 AN: 3472

East Asian (EAS) AF: 0.0455 AC: 236 AN: 5184

South Asian (SAS) AF: 0.0355 AC: 171 AN: 4822

European-Finnish (FIN) AF: 0.0419 AC: 445 AN: 10612

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0358 AC: 2438 AN: 68014

Other (OTH) AF: 0.0393 AC: 83 AN: 2114

Alfa AF: 0.0311 Hom.: 12

Bravo AF: 0.0264

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.1
DANN	Benign	0.82
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs305520; hg19: chr3-12016557;