4-13008363-A-G

Position:

• chr4-13008363-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.344 in 152,002 control chromosomes in the GnomAD database, including 9,289 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 0.34 (9289 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.74

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.424 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52281 AN: 151884 Hom.: 9281 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.344 AC: 52299 AN: 152002 Hom.: 9289 Cov.: 32 AF XY: 0.343 AC XY: 25490 AN XY: 74284

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.439

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.321

Alfa AF: 0.369 Hom.: 17482

Bravo AF: 0.332

Asia WGS AF: 0.374 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	18
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2056116; hg19: chr4-13009987;