rs4669584

Positions:

• chr2-10437773-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 0.219 in 152,158 control chromosomes in the GnomAD database, including 3,998 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 0.22 (3998 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.301 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: 0.219 AC: 33260 AN: 152040 Hom.: 3967 Cov.: 33

Gnomad AFR AF: 0.305

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0747

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.219 AC: 33344 AN: 152158 Hom.: 3998 Cov.: 33 AF XY: 0.225 AC XY: 16761 AN XY: 74374

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0745

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.204

Alfa AF: 0.213 Hom.: 799

Bravo AF: 0.212

Asia WGS AF: 0.212 AC: 738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4669584; hg19: chr2-10577899;