rs1349282

chr3-22606600-G-A

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 0.499 in 152,054 control chromosomes in the GnomAD database, including 20,645 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 0.50 (20645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 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: 0.498 AC: 75723 AN: 151936 Hom.: 20605 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.499 AC: 75813 AN: 152054 Hom.: 20645 Cov.: 32 AF XY: 0.494 AC XY: 36691 AN XY: 74310

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.327

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.481

Alfa AF: 0.431 Hom.: 20395

Bravo AF: 0.513

Asia WGS AF: 0.454 AC: 1583 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.2
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1349282; hg19: chr3-22648091;