rs1438545

Variant names:

• chr3-105333560-A-G
• rs1438545

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.128 AC: 5324 AN: 41512

American (AMR) AF: 0.167 AC: 2541 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 785 AN: 3462

East Asian (EAS) AF: 0.0867 AC: 450 AN: 5188

South Asian (SAS) AF: 0.203 AC: 976 AN: 4812

European-Finnish (FIN) AF: 0.268 AC: 2838 AN: 10574

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20096 AN: 67876

Other (OTH) AF: 0.213 AC: 449 AN: 2110

Alfa AF: 0.245 Hom.: 882

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
PhyloP100		-0.033

Splicing

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

Other links and lift over

dbSNP: rs1438545; hg19: chr3-105052404;