rs1344869

chr3-21266109-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 0.0811 in 152,066 control chromosomes in the GnomAD database, including 1,380 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 0.081 (1380 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 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: 0.0809 AC: 12300 AN: 151948 Hom.: 1368 Cov.: 32

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0936

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

GnomAD4 genome AF: 0.0811 AC: 12336 AN: 152066 Hom.: 1380 Cov.: 32 AF XY: 0.0871 AC XY: 6472 AN XY: 74342

Gnomad4 AFR AF: 0.0607

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.0265

Gnomad4 NFE AF: 0.0323

Gnomad4 OTH AF: 0.0964

Alfa AF: 0.0974 Hom.: 375

Bravo AF: 0.103

Asia WGS AF: 0.233 AC: 810 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.3
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1344869; hg19: chr3-21307601;