3-65233420-C-T

Variant names:

• chr3-65233420-C-T
• rs1482590

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 0.278 in 151,954 control chromosomes in the GnomAD database, including 6,749 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 0.28 (6749 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42136 AN: 151834 Hom.: 6739 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.278 AC: 42183 AN: 151954 Hom.: 6749 Cov.: 32 AF XY: 0.277 AC XY: 20548 AN XY: 74258

African (AFR) AF: 0.417 AC: 17244 AN: 41378

American (AMR) AF: 0.239 AC: 3641 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3464

East Asian (EAS) AF: 0.398 AC: 2061 AN: 5176

South Asian (SAS) AF: 0.383 AC: 1844 AN: 4814

European-Finnish (FIN) AF: 0.114 AC: 1203 AN: 10558

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.209 AC: 14189 AN: 67986

Other (OTH) AF: 0.297 AC: 626 AN: 2110

Alfa AF: 0.230 Hom.: 5553

Bravo AF: 0.294

Asia WGS AF: 0.361 AC: 1251 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.5
DANN	Benign	0.66
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs1482590; hg19: chr3-65219095;