3-145606706-G-A

Variant names:

• chr3-145606706-G-A
• rs10935575

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 0.227 in 151,882 control chromosomes in the GnomAD database, including 4,247 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 0.23 (4247 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34470 AN: 151764 Hom.: 4243 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.227 AC: 34485 AN: 151882 Hom.: 4247 Cov.: 31 AF XY: 0.220 AC XY: 16345 AN XY: 74196

African (AFR) AF: 0.165 AC: 6821 AN: 41442

American (AMR) AF: 0.201 AC: 3062 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1055 AN: 3466

East Asian (EAS) AF: 0.105 AC: 542 AN: 5152

South Asian (SAS) AF: 0.170 AC: 820 AN: 4820

European-Finnish (FIN) AF: 0.165 AC: 1737 AN: 10546

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19570 AN: 67940

Other (OTH) AF: 0.241 AC: 506 AN: 2102

Alfa AF: 0.256 Hom.: 670

Bravo AF: 0.229

Asia WGS AF: 0.130 AC: 455 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.3
DANN	Benign	0.95
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs10935575; hg19: chr3-145324493;