chr3-146553583-G-A

Variant names:

• chr3-146553583-G-A
• rs13074501

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 0.429 in 151,812 control chromosomes in the GnomAD database, including 14,484 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 0.43 (14484 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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: 0.429 AC: 65100 AN: 151694 Hom.: 14438 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.429 AC: 65203 AN: 151812 Hom.: 14484 Cov.: 31 AF XY: 0.430 AC XY: 31924 AN XY: 74168

African (AFR) AF: 0.531 AC: 21989 AN: 41378

American (AMR) AF: 0.407 AC: 6201 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1226 AN: 3464

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5164

South Asian (SAS) AF: 0.362 AC: 1742 AN: 4810

European-Finnish (FIN) AF: 0.490 AC: 5151 AN: 10512

Middle Eastern (MID) AF: 0.317 AC: 92 AN: 290

European-Non Finnish (NFE) AF: 0.393 AC: 26678 AN: 67934

Other (OTH) AF: 0.392 AC: 827 AN: 2110

Alfa AF: 0.419 Hom.: 2129

Bravo AF: 0.425

Asia WGS AF: 0.306 AC: 1066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.52
PhyloP100		0.061

Splicing

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

Other links and lift over

dbSNP: rs13074501; hg19: chr3-146271370;