rs13139027

Positions:

• chr4-4924439-G-A

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 0.0627 in 152,194 control chromosomes in the GnomAD database, including 315 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 0.063 (315 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.4924439G>A		intergenic_region
LOC101928306	NR_125893.1	n.353+3279G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0625 AC: 9508 AN: 152076 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0887

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.0407

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0627 AC: 9544 AN: 152194 Hom.: 315 Cov.: 32 AF XY: 0.0606 AC XY: 4507 AN XY: 74390

Gnomad4 AFR AF: 0.0568

Gnomad4 AMR AF: 0.0888

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0270

Gnomad4 FIN AF: 0.0407

Gnomad4 NFE AF: 0.0720

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0699 Hom.: 546

Bravo AF: 0.0671

Asia WGS AF: 0.0240 AC: 83 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13139027; hg19: chr4-4926166;