rs4669226

chr2-7913466-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 0.052 in 152,220 control chromosomes in the GnomAD database, including 285 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 0.052 (285 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0837 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: 0.0520 AC: 7913 AN: 152102 Hom.: 285 Cov.: 33

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0683

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0894

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0691

Gnomad OTH AF: 0.0640

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

GnomAD4 genome AF: 0.0520 AC: 7917 AN: 152220 Hom.: 285 Cov.: 33 AF XY: 0.0508 AC XY: 3781 AN XY: 74412

Gnomad4 AFR AF: 0.0245

Gnomad4 AMR AF: 0.0682

Gnomad4 ASJ AF: 0.0775

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0908

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0691

Gnomad4 OTH AF: 0.0633

Alfa AF: 0.0677 Hom.: 184

Bravo AF: 0.0551

Asia WGS AF: 0.0360 AC: 127 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.47
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4669226; hg19: chr2-8053597;