rs604222

chr3-193865921-G-Achr3-193865921-G-Cchr3-193865921-G-T

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 0.181 in 152,060 control chromosomes in the GnomAD database, including 2,567 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 (2567 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.254 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: 0.181 AC: 27440 AN: 151942 Hom.: 2554 Cov.: 33

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.181 AC: 27486 AN: 152060 Hom.: 2567 Cov.: 33 AF XY: 0.180 AC XY: 13356 AN XY: 74340

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.208

Alfa AF: 0.184 Hom.: 5336

Bravo AF: 0.182

Asia WGS AF: 0.222 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.3
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs604222; hg19: chr3-193583710;