rs3813226

Positions:

• chr2-73289653-G-A
• chr2-73289653-G-C

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 0.177 in 152,182 control chromosomes in the GnomAD database, including 3,909 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 0.18 (3909 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.172

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.176 AC: 26834 AN: 152064 Hom.: 3895 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0602

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.177 AC: 26887 AN: 152182 Hom.: 3909 Cov.: 33 AF XY: 0.179 AC XY: 13307 AN XY: 74418

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.0556

Gnomad4 NFE AF: 0.0602

Gnomad4 OTH AF: 0.165

Alfa AF: 0.107 Hom.: 346

Bravo AF: 0.198

Asia WGS AF: 0.325 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.7
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813226; hg19: chr2-73516781;