4-184086240-A-T

Position:

• chr4-184086240-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.184086240A>T		intergenic_region
LOC124900826	XR_007058415.1	n.2027+4805A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.570

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.310

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4862307; hg19: chr4-185007393;