3-83856267-C-T

Variant names:

• chr3-83856267-C-T
• rs4574309
• XR_941009.2:n.54-235G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_941009.2(LOC105377187):​n.54-235G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,430 control chromosomes in the GnomAD database, including 16,343 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 0.44 (16343 hom., cov: 31)
• Consequence: LOC105377187 XR_941009.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 1 publications found

Genes affected

LOC105377187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 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: 0.444 AC: 67147 AN: 151312 Hom.: 16328 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.444 AC: 67192 AN: 151430 Hom.: 16343 Cov.: 31 AF XY: 0.446 AC XY: 32969 AN XY: 73984

African (AFR) AF: 0.226 AC: 9354 AN: 41400

American (AMR) AF: 0.541 AC: 8201 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1776 AN: 3456

East Asian (EAS) AF: 0.545 AC: 2811 AN: 5156

South Asian (SAS) AF: 0.484 AC: 2327 AN: 4812

European-Finnish (FIN) AF: 0.475 AC: 5002 AN: 10520

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.533 AC: 36062 AN: 67600

Other (OTH) AF: 0.478 AC: 1009 AN: 2110

Alfa AF: 0.506 Hom.: 10815

Bravo AF: 0.436

Asia WGS AF: 0.547 AC: 1898 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.088
DANN	Benign	0.52
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs4574309; hg19: chr3-83905418;