chr3-1590669-C-T

Variant names:

• chr3-1590669-C-T
• rs4684256

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 0.207 in 151,444 control chromosomes in the GnomAD database, including 4,086 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 0.21 (4086 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.206
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

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: 0.207 AC: 31348 AN: 151328 Hom.: 4086 Cov.: 31

Gnomad AFR AF: 0.0861

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.0103

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.207 AC: 31336 AN: 151444 Hom.: 4086 Cov.: 31 AF XY: 0.203 AC XY: 14988 AN XY: 74008

African (AFR) AF: 0.0860 AC: 3555 AN: 41354

American (AMR) AF: 0.176 AC: 2668 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 674 AN: 3462

East Asian (EAS) AF: 0.0103 AC: 53 AN: 5152

South Asian (SAS) AF: 0.121 AC: 583 AN: 4800

European-Finnish (FIN) AF: 0.267 AC: 2800 AN: 10494

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20213 AN: 67678

Other (OTH) AF: 0.187 AC: 395 AN: 2108

Alfa AF: 0.264 Hom.: 23339

Bravo AF: 0.195

Asia WGS AF: 0.0580 AC: 203 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs4684256; hg19: chr3-1632353;