rs1438545

chr3-105333560-A-G

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 0.222 in 152,000 control chromosomes in the GnomAD database, including 4,176 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 0.22 (4176 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.293 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: 0.222 AC: 33689 AN: 151882 Hom.: 4180 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0865

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.222 AC: 33679 AN: 152000 Hom.: 4176 Cov.: 31 AF XY: 0.217 AC XY: 16156 AN XY: 74318

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0867

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.213

Alfa AF: 0.248 Hom.: 875

Bravo AF: 0.206

Asia WGS AF: 0.124 AC: 433 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.5
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1438545; hg19: chr3-105052404;