rs1450534

Variant names:

• chr3-161469877-G-A
• rs1450534

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 0.109 in 152,132 control chromosomes in the GnomAD database, including 2,035 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 0.11 (2035 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.109 AC: 16510 AN: 152014 Hom.: 2024 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0738

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0828

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.00621

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0708

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

GnomAD4 genome AF: 0.109 AC: 16554 AN: 152132 Hom.: 2035 Cov.: 32 AF XY: 0.109 AC XY: 8073 AN XY: 74396

African (AFR) AF: 0.300 AC: 12448 AN: 41462

American (AMR) AF: 0.0737 AC: 1126 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3472

East Asian (EAS) AF: 0.0830 AC: 428 AN: 5156

South Asian (SAS) AF: 0.174 AC: 838 AN: 4822

European-Finnish (FIN) AF: 0.00621 AC: 66 AN: 10620

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0203 AC: 1379 AN: 67998

Other (OTH) AF: 0.0705 AC: 149 AN: 2112

Alfa AF: 0.0779 Hom.: 189

Bravo AF: 0.119

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.63
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs1450534; hg19: chr3-161187665;