4-13007856-A-G

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 0.906 in 152,228 control chromosomes in the GnomAD database, including 62,515 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 0.91 (62515 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.927 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: 0.906 AC: 137798 AN: 152110 Hom.: 62462 Cov.: 32

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.940

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.906 AC: 137909 AN: 152228 Hom.: 62515 Cov.: 32 AF XY: 0.906 AC XY: 67443 AN XY: 74412

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.940

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.906

Alfa AF: 0.894 Hom.: 8675

Bravo AF: 0.911

Asia WGS AF: 0.887 AC: 3079 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	14
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2670760; hg19: chr4-13009480;