4-184086240-A-T

Variant names:

• chr4-184086240-A-T
• rs4862307
• XR_007058415.1:n.2027+4805A>T

Variant summary

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

The XR_007058415.1(LOC124900826):​n.2027+4805A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,184 control chromosomes in the GnomAD database, including 7,906 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 0.29 (7906 hom., cov: 33)
• Consequence: LOC124900826 XR_007058415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760
• Publications: 2 publications found

Genes affected

LOC124900826 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 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: 0.293 AC: 44529 AN: 152066 Hom.: 7890 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.293 AC: 44559 AN: 152184 Hom.: 7906 Cov.: 33 AF XY: 0.301 AC XY: 22412 AN XY: 74386

African (AFR) AF: 0.103 AC: 4268 AN: 41530

American (AMR) AF: 0.411 AC: 6283 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3468

East Asian (EAS) AF: 0.570 AC: 2951 AN: 5176

South Asian (SAS) AF: 0.442 AC: 2132 AN: 4822

European-Finnish (FIN) AF: 0.358 AC: 3789 AN: 10576

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22952 AN: 68006

Other (OTH) AF: 0.310 AC: 655 AN: 2112

Alfa AF: 0.210 Hom.: 550

Bravo AF: 0.289

Asia WGS AF: 0.476 AC: 1654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs4862307; hg19: chr4-185007393;