rs2219610

Variant names:

• chr3-30721169-G-A
• rs2219610

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 0.356 in 152,064 control chromosomes in the GnomAD database, including 10,225 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 0.36 (10225 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 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: 0.356 AC: 54072 AN: 151946 Hom.: 10221 Cov.: 33

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.356 AC: 54101 AN: 152064 Hom.: 10225 Cov.: 33 AF XY: 0.352 AC XY: 26185 AN XY: 74332

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.311

Alfa AF: 0.349 Hom.: 1816

Bravo AF: 0.349

Asia WGS AF: 0.241 AC: 839 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	15
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2219610; hg19: chr3-30762661;