rs4669226

Variant names:

• chr2-7913466-A-G
• rs4669226

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0245 AC: 1018 AN: 41560

American (AMR) AF: 0.0682 AC: 1044 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5184

South Asian (SAS) AF: 0.0908 AC: 438 AN: 4826

European-Finnish (FIN) AF: 0.0211 AC: 223 AN: 10556

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0691 AC: 4698 AN: 68000

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0608 Hom.: 259

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
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs4669226; hg19: chr2-8053597;