3-175812592-T-G

Variant names:

• chr3-175812592-T-G
• rs4894733

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 0.0818 in 136,766 control chromosomes in the GnomAD database, including 644 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 0.082 (644 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

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: 0.0816 AC: 11151 AN: 136642 Hom.: 631 Cov.: 31

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0433

Gnomad NFE AF: 0.0582

Gnomad OTH AF: 0.0720

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

GnomAD4 genome AF: 0.0818 AC: 11186 AN: 136766 Hom.: 644 Cov.: 31 AF XY: 0.0882 AC XY: 5938 AN XY: 67348

African (AFR) AF: 0.0455 AC: 1655 AN: 36392

American (AMR) AF: 0.198 AC: 2830 AN: 14296

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 317 AN: 3148

East Asian (EAS) AF: 0.144 AC: 668 AN: 4628

South Asian (SAS) AF: 0.164 AC: 713 AN: 4360

European-Finnish (FIN) AF: 0.114 AC: 1155 AN: 10104

Middle Eastern (MID) AF: 0.0210 AC: 5 AN: 238

European-Non Finnish (NFE) AF: 0.0582 AC: 3542 AN: 60908

Other (OTH) AF: 0.0806 AC: 152 AN: 1886

Alfa AF: 0.0652 Hom.: 1053

Bravo AF: 0.0788

Asia WGS AF: 0.163 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.59
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs4894733; hg19: chr3-175530380;